Serious Event Sequence

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

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

1# Reference solution for the yamaa benchmark adam-adae-serious-sequence (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# Number the subject's serious events in onset order, so the earliest16# carries 1. Events sharing one onset date follow collection order, and17# a serious event with no onset date is numbered last.18numbered <- ae |>19  filter(AESER %in% "Y") |>20  mutate(ASTDT = if_else(is.na(AESTDTC) | AESTDTC == "", NA_character_, AESTDTC)) |>21  arrange(USUBJID, is.na(ASTDT), ASTDT, AESEQ) |>22  group_by(USUBJID) |>23  mutate(SERSEQ = row_number()) |>24  ungroup() |>25  select(USUBJID, AESEQ, SERSEQ)2627adae <- ae |>28  mutate(ASTDT = if_else(is.na(AESTDTC) | AESTDTC == "", NA_character_, AESTDTC)) |>29  left_join(numbered, by = c("USUBJID", "AESEQ")) |>30  select(STUDYID, USUBJID, AESEQ, AESER, ASTDT, SERSEQ)3132dir.create("/app/output", showWarnings = FALSE)33write_csv(adae, "/app/output/adae.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adae-serious-sequence (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 1.67import csv8from pathlib import Path910INPUT_DIR = Path("/app/input")11OUTPUT_DIR = Path("/app/output")121314def main():15    with open(INPUT_DIR / "ae.csv", newline="") as f:16        rows = list(csv.DictReader(f))1718    # ASTDT is the start date collected in AESTDTC, blank when none.19    for row in rows:20        row["ASTDT"] = (row.get("AESTDTC") or "").strip()21        row["SERSEQ"] = ""2223    # SERSEQ numbers each subject's serious events (AESER "Y") from 1,24    # ordered by ASTDT with AESEQ breaking ties; serious events with no25    # ASTDT come after every dated one, in AESEQ order among themselves.26    serious = {}27    for idx, row in enumerate(rows):28        if (row.get("AESER") or "").strip() == "Y":29            serious.setdefault(row["USUBJID"], []).append(idx)3031    for idxs in serious.values():32        def sort_key(i):33            r = rows[i]34            return (0 if r["ASTDT"] else 1, r["ASTDT"], int(r["AESEQ"]))3536        for n, i in enumerate(sorted(idxs, key=sort_key), start=1):37            rows[i]["SERSEQ"] = str(n)3839    fieldnames = ["STUDYID", "USUBJID", "AESEQ", "AESER", "ASTDT", "SERSEQ"]40    OUTPUT_DIR.mkdir(parents=True, exist_ok=True)41    with open(OUTPUT_DIR / "adae.csv", "w", newline="") as f:42        writer = csv.DictWriter(f, fieldnames=fieldnames)43        writer.writeheader()44        for row in rows:45            writer.writerow({k: row.get(k, "") for k in fieldnames})464748if __name__ == "__main__":49    main()

1/* opensas reference solution for the yamaa benchmark adam-adae-serious-sequence.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 AESER AESTDTC $1024;7  infile "/app/input/ae.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. AESEQ AETERM : $char1024. AESER : $char1024. AESTDTC : $char1024.;9run;1011data ordered; set ae; nodate=missing(AESTDTC); run;12proc sort data=ordered; by STUDYID USUBJID nodate AESTDTC AESEQ; run;13data result;14  length ASTDT $10;15  set ordered; by STUDYID USUBJID;16  if first.USUBJID then counter=0;17  ASTDT=AESTDTC;18  if AESER='Y' then do; counter+1; SERSEQ=counter; end;19run;2021proc sql;22  create table final as select STUDYID, USUBJID, AESEQ, AESER, ASTDT, SERSEQ from result;23quit;24proc export data=final outfile="/app/output/adae.csv" dbms=csv replace; run;