Repeated Adverse Events from ODM

1library(yamaa)23ae <- yamaa_domain("spec.yaml")$output4ae

1import yamaa23ae = yamaa.yamaa_domain("spec.yaml").output4ae

1# Reference solution for the yamaa benchmark sdtm-ae-odm-repeated (R track).2#3# Written from the benchmark's full prompt and its inputs alone, as an agent4# would write it. Harbor's oracle agent runs it to check that the prompt can5# be solved and that the grader scores a correct answer 1.67library(dplyr, warn.conflicts = FALSE)8library(readr)9library(tidyr)1011odm <- read_csv(12  "/app/input/odm.csv",13  col_types = cols(.default = col_character())14)1516# One event per AE item group occurrence: subject, visit, visit repeat, item17# group, and item group repeat key. An occurrence without a reported term18# gives no record; a repeat key reused at a later visit starts a new event.19events <- odm |>20  filter(ItemGroupOID == "IG.AE") |>21  pivot_wider(22    id_cols = c(23      StudyOID, SubjectKey, StudyEventOID, StudyEventRepeatKey,24      ItemGroupRepeatKey25    ),26    names_from = ItemOID,27    values_from = Value,28    values_fn = first29  ) |>30  mutate(31    AETERM = `IT.AE.AETERM`,32    AESTDTC = `IT.AE.AESTDTC`,33    AEENDTC = `IT.AE.AEENDTC`,34    AESEV = `IT.AE.AESEV`,35    AESER = `IT.AE.AESER`36  ) |>37  filter(!is.na(AETERM) & AETERM != "") |>38  # Visit order is screening, then baseline; then visit repeat and item39  # group repeat key. The same term in two occurrences stays two records.40  mutate(41    VISITORD = case_when(42      StudyEventOID == "SCREENING" ~ 0L,43      StudyEventOID == "BASELINE" ~ 1L,44      .default = 2L45    ),46    VISITREP = as.integer(StudyEventRepeatKey),47    IGREP = as.integer(ItemGroupRepeatKey)48  ) |>49  arrange(SubjectKey, VISITORD, VISITREP, IGREP) |>50  group_by(SubjectKey) |>51  mutate(AESEQ = row_number()) |>52  ungroup() |>53  mutate(DOMAIN = "AE", STUDYID = StudyOID, USUBJID = SubjectKey) |>54  select(55    DOMAIN, STUDYID, USUBJID, AESEQ, AETERM,56    AESTDTC, AEENDTC, AESEV, AESER57  )5859dir.create("/app/output", showWarnings = FALSE)60write_csv(events, "/app/output/ae.csv", na = "")

1# Reference solution for the yamaa benchmark sdtm-ae-odm-repeated (Python track).2#3# Written from the benchmark's full prompt and its inputs alone, as an agent4# would write it. Harbor's oracle agent runs it to check that the prompt can5# be solved and that the grader scores a correct answer 1.67from pathlib import Path89import polars as pl1011odm = pl.read_csv("/app/input/odm.csv", infer_schema=False)1213# One event per AE item group occurrence: subject, visit, visit repeat, item14# group, and item group repeat key. An occurrence without a reported term15# gives no record; a repeat key reused at a later visit starts a new event.16events = (17    odm.filter(pl.col("ItemGroupOID") == "IG.AE")18    .pivot(19        index=[20            "StudyOID",21            "SubjectKey",22            "StudyEventOID",23            "StudyEventRepeatKey",24            "ItemGroupRepeatKey",25        ],26        on="ItemOID",27        values="Value",28        aggregate_function="first",29    )30    .with_columns(31        AETERM=pl.col("IT.AE.AETERM"),32        AESTDTC=pl.col("IT.AE.AESTDTC"),33        AEENDTC=pl.col("IT.AE.AEENDTC"),34        AESEV=pl.col("IT.AE.AESEV"),35        AESER=pl.col("IT.AE.AESER"),36    )37    .filter(pl.col("AETERM").fill_null("") != "")38    # Visit order is screening, then baseline; then visit repeat and item39    # group repeat key. The same term in two occurrences stays two records.40    .with_columns(41        VISITORD=pl.when(pl.col("StudyEventOID") == "SCREENING")42        .then(0)43        .when(pl.col("StudyEventOID") == "BASELINE")44        .then(1)45        .otherwise(2),46        VISITREP=pl.col("StudyEventRepeatKey").cast(pl.Int64),47        IGREP=pl.col("ItemGroupRepeatKey").cast(pl.Int64),48    )49    .sort(["SubjectKey", "VISITORD", "VISITREP", "IGREP"])50    .with_columns(AESEQ=pl.col("SubjectKey").cum_count().over("SubjectKey"))51    .with_columns(DOMAIN=pl.lit("AE"), STUDYID=pl.col("StudyOID"), USUBJID=pl.col("SubjectKey"))52    .select(53        "DOMAIN",54        "STUDYID",55        "USUBJID",56        "AESEQ",57        "AETERM",58        "AESTDTC",59        "AEENDTC",60        "AESEV",61        "AESER",62    )63)6465Path("/app/output").mkdir(exist_ok=True)66events.write_csv("/app/output/ae.csv")

1/* opensas reference solution for the yamaa benchmark sdtm-ae-odm-repeated.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data odm;6  length StudyOID MetaDataVersionOID SubjectKey StudyEventOID StudyEventRepeatKey FormOID FormRepeatKey ItemGroupOID ItemGroupRepeatKey ItemOID Value $1024;7  infile "/app/input/odm.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input StudyOID : $char1024. MetaDataVersionOID : $char1024. SubjectKey : $char1024. StudyEventOID : $char1024. StudyEventRepeatKey : $char1024. FormOID : $char1024. FormRepeatKey : $char1024. ItemGroupOID : $char1024. ItemGroupRepeatKey : $char1024. ItemOID : $char1024. Value : $char1024.;9run;1011proc sort data=odm out=ordered; by StudyOID SubjectKey StudyEventOID StudyEventRepeatKey ItemGroupOID ItemGroupRepeatKey; run;12data wide;13  length AETERM AESTDTC AEENDTC AESEV AESER $1024;14  retain AETERM AESTDTC AEENDTC AESEV AESER;15  set ordered;16  where ItemGroupOID='IG.AE';17  by StudyOID SubjectKey StudyEventOID StudyEventRepeatKey ItemGroupOID ItemGroupRepeatKey;18  if first.ItemGroupRepeatKey then do;19    AETERM=''; AESTDTC=''; AEENDTC=''; AESEV=''; AESER='';20  end;21    if ItemOID='IT.AE.AETERM' then AETERM=Value;22  if ItemOID='IT.AE.AESTDTC' then AESTDTC=Value;23  if ItemOID='IT.AE.AEENDTC' then AEENDTC=Value;24  if ItemOID='IT.AE.AESEV' then AESEV=Value;25  if ItemOID='IT.AE.AESER' then AESER=Value;26  if last.ItemGroupRepeatKey then output;27run;28data prepared; set wide; if not missing(AETERM);29length DOMAIN $2 STUDYID USUBJID $1024; DOMAIN='AE'; STUDYID=StudyOID; USUBJID=SubjectKey;30VISITORD=2; if StudyEventOID='SCREENING' then VISITORD=0; if StudyEventOID='BASELINE' then VISITORD=1;31VISITREP=input(StudyEventRepeatKey,best32.); IGREP=input(ItemGroupRepeatKey,best32.); run;32proc sort data=prepared; by STUDYID USUBJID VISITORD VISITREP IGREP; run;33data result; set prepared; by STUDYID USUBJID; retain AESEQ;34  if first.USUBJID then AESEQ=0;35  AESEQ+1;36run;3738proc sql;39  create table final as select DOMAIN, STUDYID, USUBJID, AESEQ, AETERM, AESTDTC, AEENDTC, AESEV, AESER from result;40quit;41proc export data=final outfile="/app/output/ae.csv" dbms=csv replace; run;