Worst Severity Flags

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

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

1# Reference solution for the yamaa benchmark adam-adae-worst-severity (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)910adae_raw <- read_csv(11  "/app/input/adae_raw.csv",12  col_types = cols(AESEQ = col_integer(), ASTDT = col_date(), .default = col_character())13)1415adae <- adae_raw |>16  mutate(17    ASEVN = case_when(18      AESEV == "MILD" ~ 1L,19      AESEV == "MODERATE" ~ 2L,20      AESEV == "SEVERE" ~ 3L21    )22  )2324# The eligible event with the greatest rank per subject and term; ties break25# by earliest date, then lowest sequence. Only a treatment-emergent event26# with a graded severity is eligible.27best <- adae |>28  filter(TRTEMFL == "Y", !is.na(ASEVN)) |>29  arrange(USUBJID, AEDECOD, desc(ASEVN), ASTDT, AESEQ) |>30  distinct(USUBJID, AEDECOD, .keep_all = TRUE) |>31  select(USUBJID, AEDECOD, AESEQ) |>32  mutate(BEST = "Y")3334adae <- adae |>35  left_join(best, by = c("USUBJID", "AEDECOD", "AESEQ")) |>36  mutate(AOCCPIFL = BEST) |>37  select(38    STUDYID, USUBJID, AESEQ, AEBODSYS, AEDECOD, ASTDT, AESEV, TRTEMFL,39    ASEVN, AOCCPIFL40  )4142dir.create("/app/output", showWarnings = FALSE)43write_csv(adae, "/app/output/adae.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adae-worst-severity (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 ADAE dataset from ADAE_RAW.89One record per adverse event, with the numeric severity rank ASEVN and10AOCCPIFL flagging, per subject and preferred term, the first occurrence11of the worst severity among treatment-emergent, severity-graded events.12"""1314import csv15from pathlib import Path1617INPUT_DIR = Path("/app/input")18OUTPUT_DIR = Path("/app/output")1920SEVERITY_RANK = {"MILD": 1, "MODERATE": 2, "SEVERE": 3}2122OUTPUT_COLUMNS = [23    "STUDYID",24    "USUBJID",25    "AESEQ",26    "AEBODSYS",27    "AEDECOD",28    "ASTDT",29    "AESEV",30    "TRTEMFL",31    "ASEVN",32    "AOCCPIFL",33]343536def severity_rank(value):37    """Numeric rank of an AESEV value; None when AESEV has no value."""38    if value is None:39        return None40    return SEVERITY_RANK.get(value.strip())414243def sequence_key(value):44    """Sort key for AESEQ so the lowest sequence number wins a tie."""45    try:46        return (0, int(value), "")47    except (TypeError, ValueError):48        return (1, 0, "" if value is None else str(value))495051def occurrence_key(record):52    """Rank eligible events: worst severity, then earliest start date,53    then lowest AESEQ. A missing start date never wins a date tie."""54    astdt = (record.get("ASTDT") or "").strip()55    return (56        -record["ASEVN"],57        1 if not astdt else 0,58        astdt,59        sequence_key(record.get("AESEQ")),60    )616263def main():64    with open(INPUT_DIR / "adae_raw.csv", newline="", encoding="utf-8") as handle:65        records = list(csv.DictReader(handle))6667    for record in records:68        record["ASEVN"] = severity_rank(record.get("AESEV"))69        record["AOCCPIFL"] = ""7071    groups = {}72    for index, record in enumerate(records):73        eligible = (74            (record.get("TRTEMFL") or "").strip() == "Y"75            and record["ASEVN"] is not None76        )77        if eligible:78            key = (record.get("USUBJID"), record.get("AEDECOD"))79            groups.setdefault(key, []).append(index)8081    for indexes in groups.values():82        winner = min(indexes, key=lambda i: occurrence_key(records[i]))83        records[winner]["AOCCPIFL"] = "Y"8485    OUTPUT_DIR.mkdir(parents=True, exist_ok=True)86    with open(OUTPUT_DIR / "adae.csv", "w", newline="", encoding="utf-8") as handle:87        writer = csv.DictWriter(handle, fieldnames=OUTPUT_COLUMNS)88        writer.writeheader()89        for record in records:90            row = {column: record.get(column) or "" for column in OUTPUT_COLUMNS}91            row["ASEVN"] = "" if record["ASEVN"] is None else str(record["ASEVN"])92            writer.writerow(row)939495if __name__ == "__main__":96    main()

1/* opensas reference solution for the yamaa benchmark adam-adae-worst-severity.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data adae_raw;6  length STUDYID USUBJID AEBODSYS AEDECOD ASTDT AESEV TRTEMFL $1024;7  infile "/app/input/adae_raw.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. AESEQ AEBODSYS : $char1024. AEDECOD : $char1024. ASTDT : $char1024. AESEV : $char1024. TRTEMFL : $char1024.;9run;1011data graded;12  length ASEV $20;13  set adae_raw; NODATE=missing(ASTDT); ASEV=AESEV;14  select(ASEV); when('MILD') ASEVN=1; when('MODERATE') ASEVN=2; when('SEVERE') ASEVN=3; when('LIFE-THREATENING') ASEVN=4; otherwise ASEVN=.; end;15run;16proc sort data=graded(where=(TRTEMFL='Y' and not missing(ASEVN))) out=eligible; by STUDYID USUBJID AEDECOD descending ASEVN NODATE ASTDT AESEQ; run;17data worst; set eligible; by STUDYID USUBJID AEDECOD; if first.AEDECOD; keep STUDYID USUBJID AESEQ; run;18proc sql; create table result as select a.*,case when not missing(b.AESEQ) then 'Y' else '' end as AOCCPIFL from graded as a left join worst as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID and a.AESEQ=b.AESEQ; quit;1920proc sql;21  create table final as select STUDYID, USUBJID, AESEQ, AEBODSYS, AEDECOD, ASTDT, AESEV, TRTEMFL, ASEVN, AOCCPIFL from result;22quit;23proc export data=final outfile="/app/output/adae.csv" dbms=csv replace; run;