Subject-Level Analysis Data Submitted in SAS Transport with ADaMIG 1.1

Review ask

As a clinical trial statistician or programmer, answer three short questions in Your review: the task, the inputs and outputs, and the AI-assisted review. Agreeing with all three approves this benchmark; disagreeing with any 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: carry TRT01A, AGE, HEIGHTBL, TRTSDT and TRTSDTM into ADSL and submit it as the SAS transport file adsl.xpt, with the dates as SAS numeric dates.

Input: one pre-analysis row per subject carrying the actual treatment, age, baseline height and the collected date and time of first exposure.

Variables:

TRT01A is the actual treatment.
AGE is the age in years, shown in three positions.
HEIGHTBL is the baseline height in centimetres, shown with one decimal; missing when not measured.
TRTSDT is the date part of TRTSDTM; missing when the subject was never treated.
TRTSDTM is the date and time of first exposure; missing when the subject was never treated.

Note: in the transport file TRTSDT counts days and TRTSDTM seconds from 1 January 1960, shown as DATE9. and DATETIME20., and the data-definition document describes both as eight-byte integers with those formats. Each text variable is exactly as wide as its longest value.

The project.yaml guide declaration is ADaMIG 1.1; the data-definition document records it and points to the SAS Transport version 5 dataset.

YAML specification

1 spec file

spec.yaml

Edit105 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, TRT01A, AGE, HEIGHTBL, TRTSDT, TRTSDTM]1213columns:14  - name: STUDYID15    type: str16    label: Study Identifier17    derivation: ADSL_RAW.STUDYID18    submission:19      core: Req20      mandatory: true21      length: 2022      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: 3034      origins:35        - type: Predecessor36          description: ADSL_RAW.USUBJID3738  - name: TRT01A39    type: str40    label: Actual Treatment for Period 0141    derivation: ADSL_RAW.TRT01A42    submission:43      core: Cond44      mandatory: true45      length: 2046      origins:47        - type: Predecessor48          description: ADSL_RAW.TRT01A4950  - name: AGE51    type: int52    label: Age53    derivation: ADSL_RAW.AGE54    submission:55      core: Req56      mandatory: true57      length: 358      display_format: "3."59      origins:60        - type: Predecessor61          description: ADSL_RAW.AGE6263  - name: HEIGHTBL64    type: float65    label: Baseline Height (cm)66    derivation: ADSL_RAW.HEIGHTBL67    submission:68      core: Perm69      mandatory: false70      length: 571      significant_digits: 172      display_format: "5.1"73      origins:74        - type: Predecessor75          description: ADSL_RAW.HEIGHTBL7677  - name: TRTSDTM78    type: datetime79    label: Datetime of First Exposure to Treatment80    derivation: ADSL_RAW.TRTSDTC81    submission:82      core: Perm83      mandatory: false84      origins:85        - type: Predecessor86          description: ADSL_RAW.TRTSDTC8788  - name: TRTSDT89    type: date90    label: Date of First Exposure to Treatment91    derivation:92      to_date:93        source: TRTSDTM94    submission:95      core: Cond96      mandatory: false97      origins:98        - type: Derived99      method: Date part of TRTSDTM.100101submission:102  label: Subject-Level Analysis Dataset103  class: SUBJECT LEVEL ANALYSIS DATASET104  structure: One record per subject105  repeating: false

Inputs

Under review1 source file

input/adsl_raw.csv

Edit3 rows

input/adsl_raw.csv
STUDYID	TRT01A	AGE	HEIGHTBL	TRTSDTC
CATH	VITAMIN D3	34	172.5	2025-01-08T08:30
CATH	PLACEBO	67	—	2025-01-15T09:05:30
CATH	NOT TREATED	52	165.2	—

Expected output

Under review3 expected rows

expected/adsl.csv

Edit3 rows

expected/adsl.csv
STUDYID	TRT01A	AGE	HEIGHTBL	TRTSDT	TRTSDTM
CATH	VITAMIN D3	34	172.5	2025-01-08	2025-01-08T08:30:00
CATH	PLACEBO	67	—	2025-01-15	2025-01-15T09:05:30
CATH	NOT TREATED	52	165.2	—	—

expected/define.xml

EditDefine-XML

Define-XML 2.1.11: CATH

Example study submitting subject-level analysis data in SAS transport; CATH-01; ADaMIG 1.1

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.xpt

ADSL

ADSL variables
Variable	Label / Description	Type	Length or Display Format	Origin / Source / Method / Comment
STUDYID	Study Identifier	text	4	Predecessor; ADSL_RAW.STUDYID
USUBJID	Unique Subject Identifier	text	16	Predecessor; ADSL_RAW.USUBJID
TRT01A	Actual Treatment for Period 01	text	11	Predecessor; ADSL_RAW.TRT01A
AGE	Age	integer	3.	Predecessor; ADSL_RAW.AGE
HEIGHTBL	Baseline Height (cm)	float	5.1	Predecessor; ADSL_RAW.HEIGHTBL
TRTSDT	Date of First Exposure to Treatment	integer	DATE9.	Derived; Sponsor Date part of TRTSDTM.
TRTSDTM	Datetime of First Exposure to Treatment	integer	DATETIME20.	Predecessor; ADSL_RAW.TRTSDTC

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="Submission">
  <Study OID="STDY.CATH">
    <GlobalVariables>
      <StudyName>CATH</StudyName>
      <StudyDescription>Example study submitting subject-level analysis data in SAS transport</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="1.1" 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.TRT01A" OrderNumber="3" Mandatory="Yes"/>
        <ItemRef ItemOID="IT.ADSL.AGE" OrderNumber="4" Mandatory="Yes"/>
        <ItemRef ItemOID="IT.ADSL.HEIGHTBL" OrderNumber="5" Mandatory="No"/>
        <ItemRef ItemOID="IT.ADSL.TRTSDT" OrderNumber="6" Mandatory="No" MethodOID="MT.ADSL.TRTSDT"/>
        <ItemRef ItemOID="IT.ADSL.TRTSDTM" OrderNumber="7" Mandatory="No"/>
        <def:Class Name="SUBJECT LEVEL ANALYSIS DATASET"/>
        <def:leaf ID="LF.ADSL" xlink:href="adsl.xpt">
          <def:title>adsl.xpt</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="16" 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.TRT01A" Name="TRT01A" DataType="text" Length="11" SASFieldName="TRT01A">
        <Description>
          <TranslatedText xml:lang="en">Actual Treatment for Period 01</TranslatedText>
        </Description>
        <def:Origin Type="Predecessor">
          <Description>
            <TranslatedText xml:lang="en">ADSL_RAW.TRT01A</TranslatedText>
          </Description>
        </def:Origin>
      </ItemDef>
      <ItemDef OID="IT.ADSL.AGE" Name="AGE" DataType="integer" Length="3" SASFieldName="AGE" def:DisplayFormat="3.">
        <Description>
          <TranslatedText xml:lang="en">Age</TranslatedText>
        </Description>
        <def:Origin Type="Predecessor">
          <Description>
            <TranslatedText xml:lang="en">ADSL_RAW.AGE</TranslatedText>
          </Description>
        </def:Origin>
      </ItemDef>
      <ItemDef OID="IT.ADSL.HEIGHTBL" Name="HEIGHTBL" DataType="float" Length="5" SignificantDigits="1" SASFieldName="HEIGHTBL" def:DisplayFormat="5.1">
        <Description>
          <TranslatedText xml:lang="en">Baseline Height (cm)</TranslatedText>
        </Description>
        <def:Origin Type="Predecessor">
          <Description>
            <TranslatedText xml:lang="en">ADSL_RAW.HEIGHTBL</TranslatedText>
          </Description>
        </def:Origin>
      </ItemDef>
      <ItemDef OID="IT.ADSL.TRTSDT" Name="TRTSDT" DataType="integer" Length="8" SASFieldName="TRTSDT" def:DisplayFormat="DATE9.">
        <Description>
          <TranslatedText xml:lang="en">Date of First Exposure to Treatment</TranslatedText>
        </Description>
        <def:Origin Type="Derived" Source="Sponsor"/>
      </ItemDef>
      <ItemDef OID="IT.ADSL.TRTSDTM" Name="TRTSDTM" DataType="integer" Length="8" SASFieldName="TRTSDTM" def:DisplayFormat="DATETIME20.">
        <Description>
          <TranslatedText xml:lang="en">Datetime of First Exposure to Treatment</TranslatedText>
        </Description>
        <def:Origin Type="Predecessor">
          <Description>
            <TranslatedText xml:lang="en">ADSL_RAW.TRTSDTC</TranslatedText>
          </Description>
        </def:Origin>
      </ItemDef>
      <MethodDef OID="MT.ADSL.TRTSDT" Name="ADSL.TRTSDT" Type="Computation">
        <Description>
          <TranslatedText xml:lang="en">Date part of TRTSDTM.</TranslatedText>
        </Description>
      </MethodDef>
    </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	TRT01A	Actual Treatment for Period 01	character		Cond	Copy value from ADSL_RAW.TRT01A.	Predecessor
ADSL	AGE	Age	numeric		Req	Copy value from ADSL_RAW.AGE.	Predecessor
ADSL	HEIGHTBL	Baseline Height (cm)	numeric		Perm	Copy value from ADSL_RAW.HEIGHTBL.	Predecessor
ADSL	TRTSDTM	Datetime of First Exposure to Treatment	numeric	ISO 8601	Perm	Copy value from ADSL_RAW.TRTSDTC.	Predecessor
ADSL	TRTSDT	Date of First Exposure to Treatment	numeric	ISO 8601	Cond	Date part of TRTSDTM.	Derived

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

prompts/adam-adsl-adamig11/full.md

Edit14 lines

Following CDISC ADaM standards, use the provided ADSL_RAW dataset to create an ADSL dataset with one record per subject.

The output dataset should contain the following columns in this order: STUDYID, USUBJID, TRT01A, AGE, HEIGHTBL, TRTSDT, TRTSDTM

TRTSDTM is the first exposure date and time from ADSL_RAW.TRTSDTC, expressed as YYYY-MM-DDThh:mm:ss with seconds 00 when the collected value ends at the minute. TRTSDT is the calendar date of TRTSDTM. TRTSDT and TRTSDTM have no value for a subject who was never treated. HEIGHTBL has no value when baseline height was not measured.

Read the source datasets from /app/input and save the completed dataset as /app/output/adsl.csv.

prompts/adam-adsl-adamig11/conventions.md

Edit10 lines

Following CDISC ADaM standards, use the provided ADSL_RAW dataset to create an ADSL dataset with one record per subject.

The output dataset should contain the following columns in this order: STUDYID, USUBJID, TRT01A, AGE, HEIGHTBL, TRTSDT, TRTSDTM

TRTSDTM is expressed as YYYY-MM-DDThh:mm:ss or has no value.

Read the source datasets from /app/input and save the completed dataset as /app/output/adsl.csv.

prompts/adam-adsl-adamig11/brief.md

Edit8 lines

Following CDISC ADaM standards, use the provided ADSL_RAW dataset to create an ADSL dataset with one record per subject.

The output dataset should contain the following columns in this order: STUDYID, USUBJID, TRT01A, AGE, HEIGHTBL, TRTSDT, TRTSDTM

Read the source datasets from /app/input and save the completed dataset as /app/output/adsl.csv.

R

Edit3 lines

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

Python

Edit3 lines

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

solutions/adam-adsl-adamig11/result.R

Edit27 lines

1# Create the subject-level ADaM ADSL dataset from the supplied source.2raw <- read.csv("/app/input/adsl_raw.csv", stringsAsFactors = FALSE,3                na.strings = c("", "NA"), check.names = FALSE)45required <- c("STUDYID", "USUBJID", "TRT01A", "AGE", "HEIGHTBL", "TRTSDTC")6stopifnot(all(required %in% names(raw)), !anyNA(raw$USUBJID),7          !anyDuplicated(raw$USUBJID))89# Complete minute-resolution collection values with zero seconds.10trtsdtm <- trimws(raw$TRTSDTC)11minute_only <- !is.na(trtsdtm) &12  grepl("^[0-9]{4}-[0-9]{2}-[0-9]{2}T[0-9]{2}:[0-9]{2}$", trtsdtm)13trtsdtm[minute_only] <- paste0(trtsdtm[minute_only], ":00")14trtsdtm[is.na(trtsdtm) | trtsdtm == ""] <- NA_character_15trtsdt <- as.Date(substr(trtsdtm, 1L, 10L), format = "%Y-%m-%d")1617adsl <- data.frame(18  STUDYID = raw$STUDYID,19  USUBJID = raw$USUBJID,20  TRT01A = raw$TRT01A,21  AGE = raw$AGE,22  HEIGHTBL = raw$HEIGHTBL,23  TRTSDT = trtsdt,24  TRTSDTM = trtsdtm,25  stringsAsFactors = FALSE26)27write.csv(adsl, "/app/output/adsl.csv", row.names = FALSE, na = "")

solutions/adam-adsl-adamig11/result.py

Edit42 lines

1"""Create the subject-level ADSL dataset from ADSL_RAW."""23import csv4from datetime import datetime5from pathlib import Path678INPUT = Path("/app/input/adsl_raw.csv")9OUTPUT = Path("/app/output/adsl.csv")10COLUMNS = ["STUDYID", "USUBJID", "TRT01A", "AGE", "HEIGHTBL", "TRTSDT", "TRTSDTM"]111213def main():14    with INPUT.open(newline="", encoding="utf-8-sig") as source:15        records = list(csv.DictReader(source))1617    subjects = {}18    for raw in records:19        key = (raw["STUDYID"], raw["USUBJID"])20        if key not in subjects:21            subjects[key] = {name: raw.get(name, "") for name in COLUMNS[:5]}22            subjects[key]["TRTSDT"] = ""23            subjects[key]["TRTSDTM"] = ""24        collected = raw.get("TRTSDTC", "").strip()25        if collected:26            # Missing seconds in a collected minute-level timestamp become 00.27            exposure = datetime.fromisoformat(collected)28            timestamp = exposure.strftime("%Y-%m-%dT%H:%M:%S")29            existing = subjects[key]["TRTSDTM"]30            if not existing or timestamp < existing:31                subjects[key]["TRTSDTM"] = timestamp32                subjects[key]["TRTSDT"] = exposure.date().isoformat()3334    OUTPUT.parent.mkdir(parents=True, exist_ok=True)35    with OUTPUT.open("w", newline="", encoding="utf-8") as target:36        writer = csv.DictWriter(target, fieldnames=COLUMNS)37        writer.writeheader()38        writer.writerows(subjects.values())394041if __name__ == "__main__":42    main()

solutions/adam-adsl-adamig11/result.sas

Edit17 lines

1proc import datafile="/app/input/adsl_raw.csv" out=adsl_raw dbms=csv replace;2  getnames=yes;3run;45data adsl;6  length STUDYID $20 USUBJID $40 TRT01A $40 AGE 8 HEIGHTBL 8 TRTSDT $10 TRTSDTM $19;7  set adsl_raw;8  if not missing(TRTSDTC) then do;9    TRTSDTM=strip(TRTSDTC);10    if length(TRTSDTM)=16 then TRTSDTM=cats(TRTSDTM,':00');11    TRTSDT=substr(TRTSDTM,1,10);12  end;13  keep STUDYID USUBJID TRT01A AGE HEIGHTBL TRTSDT TRTSDTM;14run;1516proc export data=adsl outfile="/app/output/adsl.csv" dbms=csv replace;17run;

input/adsl_raw.csv

expected/adsl.csv

expected/define.xml

Define-XML 2.1.11: CATH

ADSL

Your review

Mapping spec

Agent prompt

prompts/adam-adsl-adamig11/full.md

prompts/adam-adsl-adamig11/conventions.md

prompts/adam-adsl-adamig11/brief.md

yamaa code

R

Python

Solution without yamaa

solutions/adam-adsl-adamig11/result.R

solutions/adam-adsl-adamig11/result.py

solutions/adam-adsl-adamig11/result.sas