Confirmed Response

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

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

1# Reference solution for the yamaa benchmark adam-adrs-confirmed-response (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)910rs <- read_csv(11  "/app/input/rs.csv",12  col_types = cols(13    RSSEQ = col_integer(),14    RSDTC = col_date(),15    .default = col_character()16  )17)1819# Each assessment is compared with the next one in analysis date order;20# assessments sharing a date are ordered by sequence number, so the21# higher-numbered one is zero days later and never confirms the lower.22ordered <- rs |>23  mutate(PARAMCD = "CONFRESP", ADT = RSDTC, AVALC = RSSTRESC) |>24  arrange(STUDYID, USUBJID, ADT, RSSEQ) |>25  group_by(STUDYID, USUBJID) |>26  mutate(27    NEXT_AVALC = lead(AVALC),28    NEXT_ADT = lead(ADT),29    DAYS = as.integer(NEXT_ADT - ADT),30    CONFIRMED = case_when(31      AVALC %in% "PD" ~ "Y",32      AVALC %in% c("PR", "CR") &33        NEXT_AVALC %in% c("PR", "CR") &34        !is.na(DAYS) & DAYS >= 28L ~ "Y",35      .default = "N"36    )37  ) |>38  ungroup() |>39  select(STUDYID, USUBJID, PARAMCD, RSSEQ, ADT, AVALC, CONFIRMED) |>40  arrange(USUBJID, ADT, RSSEQ)4142dir.create("/app/output", showWarnings = FALSE)43write_csv(ordered, "/app/output/adrs.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adrs-confirmed-response (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 datetime import date910INPUT_DIR = "/app/input"11OUTPUT_DIR = "/app/output"121314def parse_date(text):15    if text is None or text.strip() == "":16        return None17    return date.fromisoformat(text.strip())181920def main():21    with open(INPUT_DIR + "/rs.csv", newline="") as fh:22        rows = list(csv.DictReader(fh))2324    records = []25    for row in rows:26        records.append(27            {28                "studyid": row["STUDYID"],29                "usubjid": row["USUBJID"],30                "rsseq": int(row["RSSEQ"]),31                "adt": row["RSDTC"].strip() if row["RSDTC"] else "",32                "date": parse_date(row["RSDTC"]),33                "avalc": row["RSSTRESC"].strip() if row["RSSTRESC"] else "",34            }35        )3637    by_subject = {}38    for rec in records:39        by_subject.setdefault(rec["usubjid"], []).append(rec)4041    for subject_records in by_subject.values():42        subject_records.sort(key=lambda r: (r["date"], r["rsseq"]))43        for i, rec in enumerate(subject_records):44            nxt = subject_records[i + 1] if i + 1 < len(subject_records) else None45            if rec["avalc"] == "PD":46                rec["confirmed"] = "Y"47            elif rec["avalc"] in ("PR", "CR"):48                if (49                    nxt is not None50                    and nxt["avalc"] in ("PR", "CR")51                    and (nxt["date"] - rec["date"]).days >= 2852                ):53                    rec["confirmed"] = "Y"54                else:55                    rec["confirmed"] = "N"56            else:57                rec["confirmed"] = "N"5859    out_rows = []60    for rec in records:61        out_rows.append(62            {63                "STUDYID": rec["studyid"],64                "USUBJID": rec["usubjid"],65                "PARAMCD": "CONFRESP",66                "RSSEQ": rec["rsseq"],67                "ADT": rec["adt"],68                "AVALC": rec["avalc"],69                "CONFIRMED": rec["confirmed"],70            }71        )7273    fieldnames = ["STUDYID", "USUBJID", "PARAMCD", "RSSEQ", "ADT", "AVALC", "CONFIRMED"]74    with open(OUTPUT_DIR + "/adrs.csv", "w", newline="") as fh:75        writer = csv.DictWriter(fh, fieldnames=fieldnames)76        writer.writeheader()77        writer.writerows(out_rows)787980if __name__ == "__main__":81    main()

1/* opensas reference solution for the yamaa benchmark adam-adrs-confirmed-response.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data rs;6  length STUDYID USUBJID RSDTC RSSTRESC $1024;7  infile "/app/input/rs.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. RSSEQ RSDTC : $char1024. RSSTRESC : $char1024.;9run;1011proc sort data=rs out=ordered; by STUDYID USUBJID descending RSDTC descending RSSEQ; run;12data result;13  length PARAMCD $16 ADT $10 AVALC $1024 CONFIRMED $1 nextresult $1024 nextdate $10;14  retain nextresult nextdate;15  set ordered; by STUDYID USUBJID;16  if first.USUBJID then do; nextresult=''; nextdate=''; end;17  PARAMCD='CONFRESP'; ADT=RSDTC; AVALC=RSSTRESC; CONFIRMED='N';18  if AVALC='PD' then CONFIRMED='Y';19  else if AVALC in ('PR','CR') and nextresult in ('PR','CR') and not missing(ADT) and not missing(nextdate) and input(nextdate,yymmdd10.)-input(ADT,yymmdd10.)>=28 then CONFIRMED='Y';20  nextresult=AVALC; nextdate=ADT;21run;2223proc sql;24  create table final as select STUDYID, USUBJID, PARAMCD, RSSEQ, ADT, AVALC, CONFIRMED from result;25quit;26proc export data=final outfile="/app/output/adrs.csv" dbms=csv replace; run;