Replace One of a Study's Shared Codelists in a Submission Package

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Summary

EditUnder 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, with a data-definition document listing the coded values and decodes of each.

Input: spec.yaml reads one pre-analysis row per subject, and project.yaml lists two codelist files in order:

study/codelists.yaml holds the study's lists of planned treatments and of discontinuation reasons, which every submission package of the study shares;
codelists.yaml holds this package's own list of discontinuation reasons, under the study's code for it.

Variables:

TRT01P is the planned treatment, one of the study's coded values.
DCSREAS is the reason for discontinuation from the study, one of the package's coded values, which admit a subject lost to follow-up.

Note: a list in a later file replaces the earlier list of the same code whole: its name, its values and its decodes come from the package, and none from the study, so a subject lost to follow-up is admitted and each reason decodes as the coded value itself. The study's planned treatments are kept as the study declares them. The data-definition document lists the kept planned treatments first, where the study's file lists them, then the package's reasons, where the package's file lists them.

YAML specification

1 spec file

spec.yaml

Edit70 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADSL5keys: [STUDYID, USUBJID]6input:7  ADSL_RAW: input/adsl_raw.csv89output:10  path: adsl.csv11  columns: [STUDYID, USUBJID, TRT01P, DCSREAS]1213columns:14  - name: STUDYID15    type: str16    label: Study Identifier17    derivation: ADSL_RAW.STUDYID18    submission:19      core: Req20      mandatory: true21      length: 422      origins:23        - type: Predecessor24          description: ADSL_RAW.STUDYID2526  - name: USUBJID27    type: str28    label: Unique Subject Identifier29    derivation: ADSL_RAW.USUBJID30    submission:31      core: Req32      mandatory: true33      length: 934      origins:35        - type: Predecessor36          description: ADSL_RAW.USUBJID3738  # The study's shared planned treatments, which this package does not change.39  - name: TRT01P40    type: str41    label: Planned Treatment for Period 0142    derivation: ADSL_RAW.TRT01P43    submission:44      core: Req45      mandatory: true46      length: 1047      codelist: TRT01P48      origins:49        - type: Predecessor50          description: ADSL_RAW.TRT01P5152  # The package's own discontinuation reasons, which replace the study's.53  - name: DCSREAS54    type: str55    label: Reason for Discontinuation from Study56    derivation: ADSL_RAW.DCSREAS57    submission:58      core: Perm59      mandatory: true60      length: 2161      codelist: DCSREAS62      origins:63        - type: Predecessor64          description: ADSL_RAW.DCSREAS6566submission:67  label: Subject-Level Analysis Dataset68  class: SUBJECT LEVEL ANALYSIS DATASET69  structure: One record per subject70  repeating: false

Inputs

Under review1 source file

input/adsl_raw.csv

Edit4 rows

input/adsl_raw.csv
STUDYID	TRT01P	DCSREAS
CATH	VITAMIN D3	COMPLETED
CATH	PLACEBO	ADVERSE EVENT
CATH	VITAMIN D3	LOST TO FOLLOW-UP
CATH	PLACEBO	WITHDRAWAL BY SUBJECT

Expected output

Under review4 expected rows

expected/adsl.csv

Edit4 rows

expected/adsl.csv
STUDYID	TRT01P	DCSREAS
CATH	VITAMIN D3	COMPLETED
CATH	PLACEBO	ADVERSE EVENT
CATH	VITAMIN D3	LOST TO FOLLOW-UP
CATH	PLACEBO	WITHDRAWAL 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
Dataset	Description	Class	Structure	Purpose	Keys	Documentation	Location
ADSL	Subject-Level Analysis Dataset	SUBJECT LEVEL ANALYSIS DATASET	One record per subject	Analysis	STUDYID, USUBJID		adsl.csv

ADSL

ADSL variables
Variable	Label / Description	Type	Length or Display Format	Controlled Terms or ISO Format	Origin / Source / Method / Comment
STUDYID	Study Identifier	text	4		Predecessor; ADSL_RAW.STUDYID
USUBJID	Unique Subject Identifier	text	9		Predecessor; ADSL_RAW.USUBJID
TRT01P	Planned Treatment for Period 01	text	10	Planned Treatment for Period 01 (CL.TRT01P) PLACEBO = Placebo VITAMIN D3 = Vitamin D3 5000 IU daily	Predecessor; ADSL_RAW.TRT01P
DCSREAS	Reason for Discontinuation from Study	text	21	Reason 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 SUBJECT	Predecessor; 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

Dataset Name	Variable Name	Variable Label	Type	Codelist/Controlled Terms	Core	Computational Method	Origin
ADSL	STUDYID	Study Identifier	character		Req	Copy value from ADSL_RAW.STUDYID.	Predecessor
ADSL	USUBJID	Unique Subject Identifier	character		Req	Copy value from ADSL_RAW.USUBJID.	Predecessor
ADSL	TRT01P	Planned Treatment for Period 01	character	Planned Treatment for Period 01	Req	Copy value from ADSL_RAW.TRT01P.	Predecessor
ADSL	DCSREAS	Reason for Discontinuation from Study	character	Reason for Discontinuation from Study	Perm	Copy value from ADSL_RAW.DCSREAS.	Predecessor

Codelist ID	Name	Value	Decode	Extensible
DCSREAS	Reason for Discontinuation	ADVERSE EVENT	Adverse Event	No
DCSREAS	Reason for Discontinuation	COMPLETED	Completed	No
DCSREAS	Reason for Discontinuation	WITHDRAWAL BY SUBJECT	Withdrawal by Subject	No
TRT01P	Planned Treatment for Period 01	PLACEBO	Placebo	No
TRT01P	Planned Treatment for Period 01	VITAMIN D3	Vitamin D3 5000 IU daily	No
DCSREAS	Reason for Discontinuation from Study	ADVERSE EVENT	ADVERSE EVENT	No
DCSREAS	Reason for Discontinuation from Study	COMPLETED	COMPLETED	No
DCSREAS	Reason for Discontinuation from Study	LOST TO FOLLOW-UP	LOST TO FOLLOW-UP	No
DCSREAS	Reason for Discontinuation from Study	WITHDRAWAL BY SUBJECT	WITHDRAWAL BY SUBJECT	No

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")$spec("ADSL")$run()$output

Python