Give Each Analysis Period an End-of-Period Status

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

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

1# Reference solution for the yamaa benchmark adam-adsl-period-status (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 <- read_csv(11  "/app/input/dm.csv",12  col_types = cols(.default = col_character())13)14ex <- read_csv(15  "/app/input/ex.csv",16  col_types = cols(EXSEQ = col_integer(), .default = col_character())17)18ds <- read_csv(19  "/app/input/ds.csv",20  col_types = cols(DSSEQ = col_integer(), .default = col_character())21)2223# A subject entered a period when it has an exposure record in that24# period's epoch; its disposition event is the DISPOSITION EVENT record25# in the same epoch.26entered1 <- ex |>27  filter(EPOCH %in% "TREATMENT 1") |>28  distinct(STUDYID, USUBJID) |>29  mutate(P01EX = 1L)30entered2 <- ex |>31  filter(EPOCH %in% "TREATMENT 2") |>32  distinct(STUDYID, USUBJID) |>33  mutate(P02EX = 1L)3435event1 <- ds |>36  filter(DSCAT %in% "DISPOSITION EVENT", EPOCH %in% "TREATMENT 1") |>37  transmute(STUDYID, USUBJID, P01DECOD = DSDECOD)38event2 <- ds |>39  filter(DSCAT %in% "DISPOSITION EVENT", EPOCH %in% "TREATMENT 2") |>40  transmute(STUDYID, USUBJID, P02DECOD = DSDECOD)4142adsl <- dm |>43  left_join(entered1, by = c("STUDYID", "USUBJID")) |>44  left_join(entered2, by = c("STUDYID", "USUBJID")) |>45  left_join(event1, by = c("STUDYID", "USUBJID")) |>46  left_join(event2, by = c("STUDYID", "USUBJID")) |>47  mutate(48    EOP01STT = case_when(49      !is.na(P01EX) & !is.na(P01DECOD) & P01DECOD == "COMPLETED" ~ "COMPLETED",50      !is.na(P01EX) & !is.na(P01DECOD) ~ "DISCONTINUED",51      !is.na(P01EX) ~ "ONGOING",52      .default = NA_character_53    ),54    DCP01RS = if_else(EOP01STT %in% "DISCONTINUED", P01DECOD, NA_character_),55    EOP02STT = case_when(56      !is.na(P02EX) & !is.na(P02DECOD) & P02DECOD == "COMPLETED" ~ "COMPLETED",57      !is.na(P02EX) & !is.na(P02DECOD) ~ "DISCONTINUED",58      !is.na(P02EX) ~ "ONGOING",59      .default = NA_character_60    ),61    DCP02RS = if_else(EOP02STT %in% "DISCONTINUED", P02DECOD, NA_character_)62  ) |>63  select(STUDYID, USUBJID, EOP01STT, DCP01RS, EOP02STT, DCP02RS)6465dir.create("/app/output", showWarnings = FALSE)66write_csv(adsl, "/app/output/adsl.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adsl-period-status (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 csv8import os910INPUT_DIR = "/app/input"11OUTPUT_DIR = "/app/output"1213PERIODS = ["TREATMENT 1", "TREATMENT 2"]141516def read_csv(name):17    with open(os.path.join(INPUT_DIR, name), newline="", encoding="utf-8") as f:18        return list(csv.DictReader(f))192021def main():22    dm = read_csv("dm.csv")23    ds = read_csv("ds.csv")24    ex = read_csv("ex.csv")2526    # Dosed periods per subject: any EX record in the period's epoch.27    dosed = {}28    for row in ex:29        dosed.setdefault(row["USUBJID"], set()).add(row["EPOCH"])3031    # Disposition event per subject and period: DS record with category32    # "DISPOSITION EVENT" in the period's epoch; keep its coded term.33    event = {}34    for row in ds:35        if row["DSCAT"] == "DISPOSITION EVENT" and row["EPOCH"] in PERIODS:36            event[(row["USUBJID"], row["EPOCH"])] = row["DSDECOD"]3738    rows = []39    for subj in dm:40        usubjid = subj["USUBJID"]41        out = {"STUDYID": subj["STUDYID"], "USUBJID": usubjid}42        for i, epoch in enumerate(PERIODS, start=1):43            status_col = f"EOP0{i}STT"44            reason_col = f"DCP0{i}RS"45            decod = event.get((usubjid, epoch))46            if decod is not None:47                if decod == "COMPLETED":48                    out[status_col] = "COMPLETED"49                    out[reason_col] = ""50                else:51                    out[status_col] = "DISCONTINUED"52                    out[reason_col] = decod53            elif epoch in dosed.get(usubjid, set()):54                out[status_col] = "ONGOING"55                out[reason_col] = ""56            else:57                out[status_col] = ""58                out[reason_col] = ""59        rows.append(out)6061    fieldnames = ["STUDYID", "USUBJID", "EOP01STT", "DCP01RS", "EOP02STT", "DCP02RS"]62    os.makedirs(OUTPUT_DIR, exist_ok=True)63    with open(os.path.join(OUTPUT_DIR, "adsl.csv"), "w", newline="", encoding="utf-8") as f:64        writer = csv.DictWriter(f, fieldnames=fieldnames)65        writer.writeheader()66        writer.writerows(rows)676869if __name__ == "__main__":70    main()

1/* opensas reference solution for the yamaa benchmark adam-adsl-period-status.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data dm;6  length STUDYID USUBJID $1024;7  infile "/app/input/dm.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024.;9run;1011data ex;12  length STUDYID USUBJID EPOCH EXTRT EXSTDTC $1024;13  infile "/app/input/ex.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024. EXSEQ EPOCH : $char1024. EXTRT : $char1024. EXSTDTC : $char1024.;15run;1617data ds;18  length STUDYID USUBJID DSCAT EPOCH DSTERM DSDECOD DSSTDTC $1024;19  infile "/app/input/ds.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;20  input STUDYID : $char1024. USUBJID : $char1024. DSSEQ DSCAT : $char1024. EPOCH : $char1024. DSTERM : $char1024. DSDECOD : $char1024. DSSTDTC : $char1024.;21run;2223proc sql;24  create table entered1 as25    select distinct STUDYID, USUBJID, 1 as P01EX from ex26    where EPOCH = 'TREATMENT 1';27  create table entered2 as28    select distinct STUDYID, USUBJID, 1 as P02EX from ex29    where EPOCH = 'TREATMENT 2';30  create table event1 as31    select STUDYID, USUBJID, DSDECOD as P01DECOD from ds32    where DSCAT = 'DISPOSITION EVENT' and EPOCH = 'TREATMENT 1';33  create table event2 as34    select STUDYID, USUBJID, DSDECOD as P02DECOD from ds35    where DSCAT = 'DISPOSITION EVENT' and EPOCH = 'TREATMENT 2';36  create table joined as37    select a.STUDYID, a.USUBJID, b.P01EX, c.P02EX, d.P01DECOD, e.P02DECOD38    from dm as a39    left join entered1 as b on a.STUDYID = b.STUDYID and a.USUBJID = b.USUBJID40    left join entered2 as c on a.STUDYID = c.STUDYID and a.USUBJID = c.USUBJID41    left join event1 as d on a.STUDYID = d.STUDYID and a.USUBJID = d.USUBJID42    left join event2 as e on a.STUDYID = e.STUDYID and a.USUBJID = e.USUBJID;43quit;4445data result;46  length EOP01STT $12 DCP01RS $1024 EOP02STT $12 DCP02RS $1024;47  set joined;48  if missing(P01EX) then EOP01STT = '';49  else if P01DECOD = 'COMPLETED' then EOP01STT = 'COMPLETED';50  else if not missing(P01DECOD) then EOP01STT = 'DISCONTINUED';51  else EOP01STT = 'ONGOING';52  if EOP01STT = 'DISCONTINUED' then DCP01RS = P01DECOD;53  if missing(P02EX) then EOP02STT = '';54  else if P02DECOD = 'COMPLETED' then EOP02STT = 'COMPLETED';55  else if not missing(P02DECOD) then EOP02STT = 'DISCONTINUED';56  else EOP02STT = 'ONGOING';57  if EOP02STT = 'DISCONTINUED' then DCP02RS = P02DECOD;58run;5960proc sql;61  create table final as select STUDYID, USUBJID, EOP01STT, DCP01RS, EOP02STT, DCP02RS from result;62quit;63proc export data=final outfile="/app/output/adsl.csv" dbms=csv replace; run;