Death Date Flag

1library(yamaa)23dm <- yamaa_domain("spec.yaml")$output4dm

1import yamaa23dm = yamaa.yamaa_domain("spec.yaml").output4dm

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 1.67from pathlib import Path89import polars as pl1011dm_raw = pl.read_csv("/app/input/dm_raw.csv", infer_schema=False)12ds = pl.read_csv("/app/input/ds.csv", infer_schema=False)13ae = pl.read_csv("/app/input/ae.csv", infer_schema=False)1415ds_death = (16    ds.filter(pl.col("DSDECOD") == "DEATH")17    .with_columns(pl.col("DSSTDTC").str.to_date(strict=False))18    .filter(pl.col("DSSTDTC").is_not_null())19    .group_by("STUDYID", "USUBJID")20    .agg(pl.col("DSSTDTC").max().alias("DS_DTH"))21)2223ae_fatal = (24    ae.filter(pl.col("AEOUT") == "FATAL")25    .with_columns(pl.col("AEENDTC").str.to_date(strict=False))26    .filter(pl.col("AEENDTC").is_not_null())27    .group_by("STUDYID", "USUBJID")28    .agg(pl.col("AEENDTC").max().alias("AE_DTH"))29)3031dm = (32    dm_raw.join(ds_death, on=["STUDYID", "USUBJID"], how="left")33    .join(ae_fatal, on=["STUDYID", "USUBJID"], how="left")34    .with_columns(35        DOMAIN=pl.lit("DM"),36        DTHDTC=pl.coalesce("DS_DTH", "AE_DTH"),37    )38    .with_columns(39        DTHFL=pl.when(pl.col("DTHDTC").is_not_null())40        .then(pl.lit("Y"))41        .otherwise(None)42    )43    .select("DOMAIN", "STUDYID", "USUBJID", "DTHDTC", "DTHFL")44)4546Path("/app/output").mkdir(exist_ok=True)47dm.write_csv("/app/output/dm.csv")

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;