Post-Index Event 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-post-index (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)910ae <- read_csv(11  "/app/input/ae.csv",12  col_types = cols(AESEQ = col_integer(), .default = col_character())13)1415# Each subject's index event: the earliest start date, with the16# higher sequence number ordered after on the same date.17first_index <- ae |>18  filter(AEDECOD %in% "COVID-19", !is.na(AESTDTC), AESTDTC != "") |>19  arrange(USUBJID, AESTDTC, AESEQ) |>20  distinct(USUBJID, .keep_all = TRUE) |>21  select(USUBJID, FIRST_DT = AESTDTC, FIRST_SEQ = AESEQ)2223adae <- ae |>24  left_join(first_index, by = "USUBJID") |>25  mutate(26    ASTDT = if_else(is.na(AESTDTC) | AESTDTC == "", NA_character_, AESTDTC),27    AFTIDXFL = if_else(28      !is.na(ASTDT) & !is.na(FIRST_DT) &29        (ASTDT > FIRST_DT | (ASTDT == FIRST_DT & AESEQ > FIRST_SEQ)),30      "Y",31      NA_character_32    )33  ) |>34  select(STUDYID, USUBJID, AESEQ, AEDECOD, ASTDT, AFTIDXFL)3536dir.create("/app/output", showWarnings = FALSE)37write_csv(adae, "/app/output/adae.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adae-post-index (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 ADAE from AE: flag records strictly after each subject's8index event (first COVID-19 record by ASTDT, AESEQ breaking ties)."""910import csv11from datetime import date1213INPUT_AE = "/app/input/ae.csv"14OUTPUT_ADAE = "/app/output/adae.csv"1516COLUMNS = ["STUDYID", "USUBJID", "AESEQ", "AEDECOD", "ASTDT", "AFTIDXFL"]171819def parse_date(text):20    text = (text or "").strip()21    if not text:22        return None23    return date.fromisoformat(text)242526def main():27    with open(INPUT_AE, newline="", encoding="utf-8") as f:28        rows = list(csv.DictReader(f))2930    for row in rows:31        row["_astdt"] = parse_date(row["AESTDTC"])32        row["_aeseq"] = int(row["AESEQ"])3334    # Index event per subject: first COVID-19 record ordered by ASTDT,35    # AESEQ breaking ties; records with no start date order last.36    index = {}37    for row in rows:38        if row["AEDECOD"] != "COVID-19":39            continue40        key = (41            row["_astdt"] is None,42            row["_astdt"] or date.min,43            row["_aeseq"],44        )45        subject = row["USUBJID"]46        if subject not in index or key < index[subject][0]:47            index[subject] = (key, row)4849    out = []50    for row in rows:51        flag = ""52        subject = row["USUBJID"]53        if subject in index and row["_astdt"] is not None:54            _, idx = index[subject]55            if row["_astdt"] > idx["_astdt"] or (56                row["_astdt"] == idx["_astdt"]57                and row["_aeseq"] > idx["_aeseq"]58            ):59                flag = "Y"60        out.append(61            {62                "STUDYID": row["STUDYID"],63                "USUBJID": row["USUBJID"],64                "AESEQ": row["AESEQ"],65                "AEDECOD": row["AEDECOD"],66                "ASTDT": row["_astdt"].isoformat() if row["_astdt"] else "",67                "AFTIDXFL": flag,68            }69        )7071    with open(OUTPUT_ADAE, "w", newline="", encoding="utf-8") as f:72        writer = csv.DictWriter(f, fieldnames=COLUMNS)73        writer.writeheader()74        writer.writerows(out)757677if __name__ == "__main__":78    main()

1/* opensas reference solution for the yamaa benchmark adam-adae-post-index.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 AEDECOD AESTDTC $1024;7  infile "/app/input/ae.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. AESEQ AEDECOD : $char1024. AESTDTC : $char1024.;9run;1011proc sort data=ae(where=(AEDECOD='COVID-19' and AESTDTC ne '')) out=indices; by STUDYID USUBJID AESTDTC AESEQ; run;12data firstindex; set indices; by STUDYID USUBJID; if first.USUBJID; run;13proc sql;14  create table result as select a.*,a.AESTDTC as ASTDT,15  case when not missing(a.AESTDTC) and not missing(b.AESTDTC) and (a.AESTDTC>b.AESTDTC or (a.AESTDTC=b.AESTDTC and a.AESEQ>b.AESEQ)) then 'Y' else '' end as AFTIDXFL16  from ae as a left join firstindex as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID;17quit;1819proc sql;20  create table final as select STUDYID, USUBJID, AESEQ, AEDECOD, ASTDT, AFTIDXFL from result;21quit;22proc export data=final outfile="/app/output/adae.csv" dbms=csv replace; run;