Death Date Flag

1library(yamaa)23yamaa_spec("spec.yaml")$run()$output

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

1# Reference solution for the yamaa benchmark sdtm-dm-death (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)910dm_raw <- read_csv(11  "/app/input/dm_raw.csv",12  col_types = cols(.default = col_character())13)14ds <- read_csv(15  "/app/input/ds.csv",16  col_types = cols(.default = col_character())17)18ae <- read_csv(19  "/app/input/ae.csv",20  col_types = cols(.default = col_character())21)2223ds_death <- ds |>24  filter(DSDECOD == "DEATH") |>25  mutate(DSSTDTC = suppressWarnings(as.Date(DSSTDTC))) |>26  filter(!is.na(DSSTDTC)) |>27  group_by(STUDYID, USUBJID) |>28  summarise(DS_DTH = max(DSSTDTC), .groups = "drop")2930ae_fatal <- ae |>31  filter(AEOUT == "FATAL") |>32  mutate(AEENDTC = suppressWarnings(as.Date(AEENDTC))) |>33  filter(!is.na(AEENDTC)) |>34  group_by(STUDYID, USUBJID) |>35  summarise(AE_DTH = max(AEENDTC), .groups = "drop")3637dm <- dm_raw |>38  left_join(ds_death, by = c("STUDYID", "USUBJID")) |>39  left_join(ae_fatal, by = c("STUDYID", "USUBJID")) |>40  mutate(41    DOMAIN = "DM",42    DTHDTC = coalesce(DS_DTH, AE_DTH),43    DTHFL = ifelse(!is.na(DTHDTC), "Y", NA_character_)44  ) |>45  select(DOMAIN, STUDYID, USUBJID, DTHDTC, DTHFL)4647dir.create("/app/output", showWarnings = FALSE)48write_csv(dm, "/app/output/dm.csv", na = "")

1# Reference solution for the yamaa benchmark sdtm-dm-death (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 1.67"""Create the SDTM DM dataset with death date and death flag.89One record per subject (from DM_RAW). DTHDTC is the latest start date10among the subject's disposition records with decoded term "DEATH"11that carry a start date; if the subject has no such record, it is the12latest end date among the subject's adverse events with outcome13"FATAL" that carry an end date. DTHFL is "Y" when either source14supplies a death date, and blank otherwise.15"""1617import csv18from collections import OrderedDict19from pathlib import Path2021INPUT_DIR = Path("/app/input")22OUTPUT_DIR = Path("/app/output")232425def read_rows(name):26    with open(INPUT_DIR / name, newline="", encoding="utf-8") as handle:27        return list(csv.DictReader(handle))282930def latest_date(dates):31    """Latest non-blank ISO date string, or "" when none is present."""32    present = [d.strip() for d in dates if d and d.strip()]33    return max(present) if present else ""343536def main():37    subjects = read_rows("dm_raw.csv")38    ds_rows = read_rows("ds.csv")39    ae_rows = read_rows("ae.csv")4041    ds_death_dates = {}42    for row in ds_rows:43        if row["DSDECOD"] == "DEATH":44            ds_death_dates.setdefault(row["USUBJID"], []).append(row["DSSTDTC"])4546    ae_fatal_dates = {}47    for row in ae_rows:48        if row["AEOUT"] == "FATAL":49            ae_fatal_dates.setdefault(row["USUBJID"], []).append(row["AEENDTC"])5051    out_rows = []52    for subject in subjects:53        usubjid = subject["USUBJID"]54        dthdtc = latest_date(ds_death_dates.get(usubjid, []))55        if not dthdtc:56            dthdtc = latest_date(ae_fatal_dates.get(usubjid, []))57        out_rows.append(58            OrderedDict(59                DOMAIN="DM",60                STUDYID=subject["STUDYID"],61                USUBJID=usubjid,62                DTHDTC=dthdtc,63                DTHFL="Y" if dthdtc else "",64            )65        )6667    OUTPUT_DIR.mkdir(parents=True, exist_ok=True)68    with open(OUTPUT_DIR / "dm.csv", "w", newline="", encoding="utf-8") as handle:69        writer = csv.DictWriter(70            handle, fieldnames=["DOMAIN", "STUDYID", "USUBJID", "DTHDTC", "DTHFL"]71        )72        writer.writeheader()73        writer.writerows(out_rows)747576if __name__ == "__main__":77    main()

1/* opensas reference solution for the yamaa benchmark sdtm-dm-death.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data ae;6  length STUDYID USUBJID AETERM AEOUT AEENDTC $1024;7  infile "/app/input/ae.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. AESEQ AETERM : $char1024. AEOUT : $char1024. AEENDTC : $char1024.;9run;1011data dm_raw;12  length STUDYID USUBJID $1024;13  infile "/app/input/dm_raw.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024.;15run;1617data ds;18  length STUDYID USUBJID DSDECOD DSCAT DSSTDTC $1024;19  infile "/app/input/ds.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;20  input STUDYID : $char1024. USUBJID : $char1024. DSSEQ DSDECOD : $char1024. DSCAT : $char1024. DSSTDTC : $char1024.;21run;2223proc sql;24create table dsdeath as select STUDYID,USUBJID,max(DSSTDTC) as DSDATE from ds where DSDECOD='DEATH' and not missing(DSSTDTC) group by STUDYID,USUBJID;25create table aedeath as select STUDYID,USUBJID,max(AEENDTC) as AEDATE from ae where AEOUT='FATAL' and not missing(AEENDTC) group by STUDYID,USUBJID;26create table joined as select a.*,b.DSDATE,c.AEDATE from dm_raw a left join dsdeath b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID left join aedeath c on a.STUDYID=c.STUDYID and a.USUBJID=c.USUBJID; quit;27data result; set joined; length DOMAIN $2 DTHDTC $1024 DTHFL $1; DOMAIN='DM'; DTHDTC=coalescec(DSDATE,AEDATE); if not missing(DTHDTC) then DTHFL='Y'; run;28proc sql;29  create table final as select DOMAIN, STUDYID, USUBJID, DTHDTC, DTHFL from result;30quit;31proc export data=final outfile="/app/output/dm.csv" dbms=csv replace; run;