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Summary
README.mdPublic entries: Python and R. Passing coverage requires an installed inventory.
Goal: derive each adverse event's analysis start date and time
(ASTDTM), its date (ASTDT), its time of day (ASTTM) and the time
imputation flag (ASTTMF), and submit them in a SAS Transport version 5
file with the data-definition document.
Input: SDTM adverse event (AE) records with the collected start
(AESTDTC) as ISO 8601 text, collected to the second, the minute, the
hour, the day or the month.
Variables:
AETERMis the adverse event as reported.ASTDTMis the start date and time: a start collected to the hour or the minute takes zero for the rest of its time, and a start collected as a date alone takes midnight; missing when the start was not collected to the day.ASTDTis the date part ofASTDTM; missing whenASTDTMis.ASTTMis the time of day ofASTDTMcounted in seconds since midnight, so08:30:15is30615, and it is shown ashh:mm:ss; missing whenASTDTMis.ASTTMFsays which part of the start time was imputed:Hwhen the start was collected without a time,Mwhen it stops at the hour andSwhen it stops at the minute; blank when the time was collected to the second or there is no start.
Note: the SAS Transport file stores ASTTM as an eight-byte numeric
value with the SAS format TIME8., beside ASTDT with DATE9. and
ASTDTM with DATETIME20.. The data-definition document records these
formats. A time of zero flagged H is an imputed midnight rather than a
collected one.
The project.yaml guide declaration is ADaMIG 1.1; the data-definition
document records it and points to the SAS Transport version 5 dataset.
Inputs
Under review1 source fileinput/ae.csv
Edit5 rows| STUDYID | USUBJID | AESEQ | AETERM | AESTDTC |
|---|---|---|---|---|
| CATH | 1 | HEADACHE | 2025-03-04T08:30:15 | |
| CATH | 2 | NAUSEA | 2025-03-06T14:05 | |
| CATH | 1 | RASH | 2025-03-10 | |
| CATH | 2 | DIZZINESS | 2025-03 | |
| CATH | 1 | FATIGUE | 2025-03-12T21 |
Expected output
Under review5 expected rowsexpected/adae.csv
Edit5 rows| STUDYID | USUBJID | AESEQ | AETERM | ASTDTM | ASTDT | ASTTM | ASTTMF |
|---|---|---|---|---|---|---|---|
| CATH | 1 | HEADACHE | 2025-03-04T08:30:15 | 2025-03-04 | 30615 | — | |
| CATH | 2 | NAUSEA | 2025-03-06T14:05:00 | 2025-03-06 | 50700 | S | |
| CATH | 1 | RASH | 2025-03-10T00:00:00 | 2025-03-10 | 0 | H | |
| CATH | 2 | DIZZINESS | — | — | — | — | |
| CATH | 1 | FATIGUE | 2025-03-12T21:00:00 | 2025-03-12 | 75600 | M |
expected/define.xml
EditDefine-XMLDefine-XML 2.1.11: CATH
Example study submitting adverse event onset times in SAS transport; CATH-01; ADaMIG 1.1
| Dataset | Description | Class | Structure | Purpose | Keys | Documentation | Location |
|---|---|---|---|---|---|---|---|
| ADAE | Adverse Events Analysis Dataset | OCCURRENCE DATA STRUCTURE | One record per adverse event | Analysis | STUDYID, USUBJID, AESEQ | adae.xpt |
ADAE
| Variable | Label / Description | Type | Length or Display Format | Controlled Terms or ISO Format | Origin / Source / Method / Comment |
|---|---|---|---|---|---|
| STUDYID | Study Identifier | text | 4 | Predecessor; AE.STUDYID | |
| USUBJID | Unique Subject Identifier | text | 16 | Predecessor; AE.USUBJID | |
| AESEQ | Sequence Number | integer | 8 | Predecessor; AE.AESEQ | |
| AETERM | Reported Term for the Adverse Event | text | 9 | Predecessor; AE.AETERM | |
| ASTDTM | Analysis Start Date/Time | integer | DATETIME20. | Derived; Sponsor AESTDTC completed with the earliest time its collected parts admit; missing when AESTDTC carries no complete date. | |
| ASTDT | Analysis Start Date | integer | DATE9. | Derived; Sponsor Date part of ASTDTM. | |
| ASTTM | Analysis Start Time | integer | TIME8. | Derived; Sponsor Time part of ASTDTM as seconds since midnight. | |
| ASTTMF | Analysis Start Time Imputation Flag | text | 1 | Derived; Sponsor H when the start was collected without a time, M when it stops at the hour and S when it stops at the minute. |
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 adverse event onset times 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.ADAE" Name="ADAE" Purpose="Analysis" SASDatasetName="ADAE" Repeating="Yes" IsReferenceData="No" def:Structure="One record per adverse event" def:ArchiveLocationID="LF.ADAE" def:StandardOID="STD.ADaMIG">
<Description>
<TranslatedText xml:lang="en">Adverse Events Analysis Dataset</TranslatedText>
</Description>
<ItemRef ItemOID="IT.ADAE.STUDYID" OrderNumber="1" Mandatory="Yes" KeySequence="1"/>
<ItemRef ItemOID="IT.ADAE.USUBJID" OrderNumber="2" Mandatory="Yes" KeySequence="2"/>
<ItemRef ItemOID="IT.ADAE.AESEQ" OrderNumber="3" Mandatory="Yes" KeySequence="3"/>
<ItemRef ItemOID="IT.ADAE.AETERM" OrderNumber="4" Mandatory="Yes"/>
<ItemRef ItemOID="IT.ADAE.ASTDTM" OrderNumber="5" Mandatory="No" MethodOID="MT.ADAE.ASTDTM"/>
<ItemRef ItemOID="IT.ADAE.ASTDT" OrderNumber="6" Mandatory="No" MethodOID="MT.ADAE.ASTDT"/>
<ItemRef ItemOID="IT.ADAE.ASTTM" OrderNumber="7" Mandatory="No" MethodOID="MT.ADAE.ASTTM"/>
<ItemRef ItemOID="IT.ADAE.ASTTMF" OrderNumber="8" Mandatory="No" MethodOID="MT.ADAE.ASTTMF"/>
<def:Class Name="OCCURRENCE DATA STRUCTURE"/>
<def:leaf ID="LF.ADAE" xlink:href="adae.xpt">
<def:title>adae.xpt</def:title>
</def:leaf>
</ItemGroupDef>
<ItemDef OID="IT.ADAE.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">AE.STUDYID</TranslatedText>
</Description>
</def:Origin>
</ItemDef>
<ItemDef OID="IT.ADAE.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">AE.USUBJID</TranslatedText>
</Description>
</def:Origin>
</ItemDef>
<ItemDef OID="IT.ADAE.AESEQ" Name="AESEQ" DataType="integer" Length="8" SASFieldName="AESEQ">
<Description>
<TranslatedText xml:lang="en">Sequence Number</TranslatedText>
</Description>
<def:Origin Type="Predecessor">
<Description>
<TranslatedText xml:lang="en">AE.AESEQ</TranslatedText>
</Description>
</def:Origin>
</ItemDef>
<ItemDef OID="IT.ADAE.AETERM" Name="AETERM" DataType="text" Length="9" SASFieldName="AETERM">
<Description>
<TranslatedText xml:lang="en">Reported Term for the Adverse Event</TranslatedText>
</Description>
<def:Origin Type="Predecessor">
<Description>
<TranslatedText xml:lang="en">AE.AETERM</TranslatedText>
</Description>
</def:Origin>
</ItemDef>
<ItemDef OID="IT.ADAE.ASTDTM" Name="ASTDTM" DataType="integer" Length="8" SASFieldName="ASTDTM" def:DisplayFormat="DATETIME20.">
<Description>
<TranslatedText xml:lang="en">Analysis Start Date/Time</TranslatedText>
</Description>
<def:Origin Type="Derived" Source="Sponsor"/>
</ItemDef>
<ItemDef OID="IT.ADAE.ASTDT" Name="ASTDT" DataType="integer" Length="8" SASFieldName="ASTDT" def:DisplayFormat="DATE9.">
<Description>
<TranslatedText xml:lang="en">Analysis Start Date</TranslatedText>
</Description>
<def:Origin Type="Derived" Source="Sponsor"/>
</ItemDef>
<ItemDef OID="IT.ADAE.ASTTM" Name="ASTTM" DataType="integer" Length="8" SASFieldName="ASTTM" def:DisplayFormat="TIME8.">
<Description>
<TranslatedText xml:lang="en">Analysis Start Time</TranslatedText>
</Description>
<def:Origin Type="Derived" Source="Sponsor"/>
</ItemDef>
<ItemDef OID="IT.ADAE.ASTTMF" Name="ASTTMF" DataType="text" Length="1" SASFieldName="ASTTMF">
<Description>
<TranslatedText xml:lang="en">Analysis Start Time Imputation Flag</TranslatedText>
</Description>
<def:Origin Type="Derived" Source="Sponsor"/>
</ItemDef>
<MethodDef OID="MT.ADAE.ASTDTM" Name="ADAE.ASTDTM" Type="Computation">
<Description>
<TranslatedText xml:lang="en">AESTDTC completed with the earliest time its collected parts admit; missing when AESTDTC carries no complete date.</TranslatedText>
</Description>
</MethodDef>
<MethodDef OID="MT.ADAE.ASTDT" Name="ADAE.ASTDT" Type="Computation">
<Description>
<TranslatedText xml:lang="en">Date part of ASTDTM.</TranslatedText>
</Description>
</MethodDef>
<MethodDef OID="MT.ADAE.ASTTM" Name="ADAE.ASTTM" Type="Computation">
<Description>
<TranslatedText xml:lang="en">Time part of ASTDTM as seconds since midnight.</TranslatedText>
</Description>
</MethodDef>
<MethodDef OID="MT.ADAE.ASTTMF" Name="ADAE.ASTTMF" Type="Computation">
<Description>
<TranslatedText xml:lang="en">H when the start was collected without a time, M when it stops at the hour and S when it stops at the minute.</TranslatedText>
</Description>
</MethodDef>
</MetaDataVersion>
</Study>
</ODM>
Human review and assessment
| Dataset Name | Variable Name | Variable Label | Type | Codelist/Controlled Terms | Core | Computational Method | Origin |
|---|---|---|---|---|---|---|---|
| ADAE | STUDYID | Study Identifier | character | Req | Copy value from AE.STUDYID. | Predecessor | |
| ADAE | USUBJID | Unique Subject Identifier | character | Req | Copy value from AE.USUBJID. | Predecessor | |
| ADAE | AESEQ | Sequence Number | numeric | Req | Copy value from AE.AESEQ. | Predecessor | |
| ADAE | AETERM | Reported Term for the Adverse Event | character | Req | Copy value from AE.AETERM. | Predecessor | |
| ADAE | ASTDTM | Analysis Start Date/Time | numeric | ISO 8601 | Perm | AESTDTC completed with the earliest time its collected parts admit; missing when AESTDTC carries no complete date. | Derived |
| ADAE | ASTDT | Analysis Start Date | numeric | ISO 8601 | Cond | Date part of ASTDTM. | Derived |
| ADAE | ASTTM | Analysis Start Time | numeric | Perm | Time part of ASTDTM as seconds since midnight. | Derived | |
| ADAE | ASTTMF | Analysis Start Time Imputation Flag | character | H, M, S | Cond | H when the start was collected without a time, M when it stops at the hour and S when it stops at the minute. | Derived |
| Variable | Permitted values |
|---|---|
| ASTTMF | H, M, S |
| Version | Date | Author | Description | Reviewer | Sign-off |
|---|---|---|---|---|---|
| 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-adae-adamig11/full.md
Edit22 linesFollowing CDISC ADaM standards, use the provided AE dataset to create an ADAE dataset with one record per adverse event.
The output dataset should contain the following columns in this order: STUDYID, USUBJID, AESEQ, AETERM, ASTDTM, ASTDT, ASTTM, ASTTMF
ASTDTM is the start date and time from AESTDTC: a start collected to the second has its collected value, a start collected to the minute has seconds 00, a start collected to the hour has minutes and seconds 00, and a complete date without a time has time 00:00:00. ASTDTM has no value when AESTDTC lacks a complete calendar date.
ASTDT is the calendar date of ASTDTM and ASTTM is its time of day as whole seconds since midnight; both have no value when ASTDTM has no value.
ASTTMF is "H" for a start collected as a complete date without a time, "M" for a start collected to the hour, and "S" for a start collected to the minute. ASTTMF has no value when the start was collected to the second or ASTDTM has no value. An ASTTM of 0 with ASTTMF "H" is imputed midnight.
Read the source datasets from /app/input and save the completed dataset as /app/output/adae.csv.
prompts/adam-adae-adamig11/conventions.md
Edit10 linesFollowing CDISC ADaM standards, use the provided AE dataset to create an ADAE dataset with one record per adverse event.
The output dataset should contain the following columns in this order: STUDYID, USUBJID, AESEQ, AETERM, ASTDTM, ASTDT, ASTTM, ASTTMF
ASTTMF is "H", "M", or "S", or has no value.
Read the source datasets from /app/input and save the completed dataset as /app/output/adae.csv.
prompts/adam-adae-adamig11/brief.md
Edit8 linesFollowing CDISC ADaM standards, use the provided AE dataset to create an ADAE dataset with one record per adverse event.
The output dataset should contain the following columns in this order: STUDYID, USUBJID, AESEQ, AETERM, ASTDTM, ASTDT, ASTTM, ASTTMF
Read the source datasets from /app/input and save the completed dataset as /app/output/adae.csv.
R
Edit3 lineslibrary(yamaa)yamaa_project("project.yaml")$spec("ADAE")$run()$outputPython
Edit3 linesimport yamaayamaa.project("project.yaml").spec("ADAE").run().outputsolutions/adam-adae-adamig11/result.R
Edit38 lines# Derive ADaM adverse-event start date/time and time-imputation flags.ae <- read.csv("/app/input/ae.csv", stringsAsFactors = FALSE, check.names = FALSE, na.strings = c("", "NA"))required <- c("STUDYID", "USUBJID", "AESEQ", "AETERM", "AESTDTC")stopifnot(all(required %in% names(ae)))n <- nrow(ae)adae <- ae[c("STUDYID", "USUBJID", "AESEQ", "AETERM")]adae$ASTDTM <- rep(NA_character_, n)adae$ASTDT <- rep(NA_character_, n)adae$ASTTM <- rep(NA_integer_, n)adae$ASTTMF <- rep(NA_character_, n)for (i in seq_len(n)) { dtc <- ae$AESTDTC[i] if (is.na(dtc)) next # Each accepted form must contain a complete calendar date. if (!grepl("^[0-9]{4}-[0-9]{2}-[0-9]{2}(T[0-9]{2}(:[0-9]{2}(:[0-9]{2})?)?)?$", dtc)) next date_text <- substr(dtc, 1L, 10L) parsed_date <- as.Date(date_text, format = "%Y-%m-%d") if (is.na(parsed_date) || format(parsed_date, "%Y-%m-%d") != date_text) next precision <- nchar(dtc) hour <- if (precision >= 13L) as.integer(substr(dtc, 12L, 13L)) else 0L minute <- if (precision >= 16L) as.integer(substr(dtc, 15L, 16L)) else 0L second <- if (precision >= 19L) as.integer(substr(dtc, 18L, 19L)) else 0L if (hour > 23L || minute > 59L || second > 59L) next adae$ASTDTM[i] <- sprintf("%sT%02d:%02d:%02d", date_text, hour, minute, second) adae$ASTDT[i] <- date_text adae$ASTTM[i] <- hour * 3600L + minute * 60L + second adae$ASTTMF[i] <- switch(as.character(precision), `10` = "H", `13` = "M", `16` = "S", NA_character_)}stopifnot(nrow(adae) == nrow(ae), identical(names(adae), c("STUDYID", "USUBJID", "AESEQ", "AETERM", "ASTDTM", "ASTDT", "ASTTM", "ASTTMF")))dir.create("/app/output", showWarnings = FALSE)write.csv(adae, "/app/output/adae.csv", row.names = FALSE, na = "")solutions/adam-adae-adamig11/result.py
Edit74 lines"""Create the event-level ADAE start datetime analysis variables."""import csvimport refrom datetime import datetimefrom pathlib import PathCOLUMNS = [ "STUDYID", "USUBJID", "AESEQ", "AETERM", "ASTDTM", "ASTDT", "ASTTM", "ASTTMF",]START_PATTERN = re.compile( r"(\d{4})-(\d{2})-(\d{2})(?:T(\d{2})(?::(\d{2})(?::(\d{2}))?)?)?")def derive_start(value): """Impute only uncollected time components of a complete calendar date.""" match = START_PATTERN.fullmatch((value or "").strip()) if match is None: return {column: "" for column in COLUMNS[4:]} year, month, day, hour, minute, second = match.groups() try: start = datetime( int(year), int(month), int(day), int(hour or 0), int(minute or 0), int(second or 0), ) except ValueError: return {column: "" for column in COLUMNS[4:]} flag = ( "H" if hour is None else "M" if minute is None else "S" if second is None else "" ) return { "ASTDTM": start.isoformat(timespec="seconds"), "ASTDT": start.date().isoformat(), "ASTTM": start.hour * 3600 + start.minute * 60 + start.second, "ASTTMF": flag, }def main(): output_path = Path("/app/output/adae.csv") output_path.parent.mkdir(parents=True, exist_ok=True) with Path("/app/input/ae.csv").open(newline="", encoding="utf-8-sig") as source: with output_path.open("w", newline="", encoding="utf-8") as target: writer = csv.DictWriter(target, fieldnames=COLUMNS) writer.writeheader() for event in csv.DictReader(source): row = {column: event.get(column, "") for column in COLUMNS[:4]} row.update(derive_start(event.get("AESTDTC"))) writer.writerow(row)if __name__ == "__main__": main()solutions/adam-adae-adamig11/result.sas
Edit40 linesproc import datafile="/app/input/ae.csv" out=ae dbms=csv replace; guessingrows=max;run;data adae; length STUDYID $40 USUBJID $80 AESEQ 8 AETERM $200 ASTDTM $19 ASTDT $10 ASTTM 8 ASTTMF $1; set ae; ASTDTM = ''; ASTDT = ''; ASTTM = .; ASTTMF = ''; _length = length(strip(AESTDTC)); if _length >= 10 then do; _date = input(substr(AESTDTC,1,10),yymmdd10.); if not missing(_date) then do; _hour = 0; _minute = 0; _second = 0; if _length = 10 then ASTTMF = 'H'; else if _length >= 13 then do; _hour = input(substr(AESTDTC,12,2),2.); if _length = 13 then ASTTMF = 'M'; else if _length >= 16 then do; _minute = input(substr(AESTDTC,15,2),2.); if _length = 16 then ASTTMF = 'S'; else if _length >= 19 then _second = input(substr(AESTDTC,18,2),2.); end; end; _datetime = dhms(_date,_hour,_minute,_second); ASTDTM = put(_datetime,e8601dt19.); ASTDT = put(datepart(_datetime),yymmdd10.); ASTTM = timepart(_datetime); end; end; keep STUDYID USUBJID AESEQ AETERM ASTDTM ASTDT ASTTM ASTTMF;run;proc export data=adae outfile="/app/output/adae.csv" dbms=csv replace;run;
yamaa