Flag Any Reported Dose Adjustment

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

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

1# Reference solution for the yamaa benchmark adam-adsl-dose-adjustment (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)9library(stringr)1011base <- read_csv(12  "/app/input/adsl.csv",13  col_types = cols(.default = col_character())14)15ex <- read_csv(16  "/app/input/ex.csv",17  col_types = cols(.default = col_character())18)19ec <- read_csv(20  "/app/input/ec.csv",21  col_types = cols(.default = col_character())22)23fa <- read_csv(24  "/app/input/fa.csv",25  col_types = cols(.default = col_character())26)2728# A record reports an adjustment with a filled value; findings-about rows29# qualify only for dose adjustment occurrences with a Y result.30ex_adj <- ex |>31  filter(!is.na(EXADJ), str_trim(EXADJ) != "") |>32  distinct(STUDYID, USUBJID) |>33  mutate(.ex_adj = TRUE)34ec_adj <- ec |>35  filter(!is.na(ECADJ), str_trim(ECADJ) != "") |>36  distinct(STUDYID, USUBJID) |>37  mutate(.ec_adj = TRUE)38fa_adj <- fa |>39  filter(FATESTCD %in% "OCCUR", FAOBJ %in% "DOSE ADJUSTMENT", FASTRESC %in% "Y") |>40  distinct(STUDYID, USUBJID) |>41  mutate(.fa_adj = TRUE)4243ex_any <- ex |> distinct(STUDYID, USUBJID) |> mutate(.ex_any = TRUE)44ec_any <- ec |> distinct(STUDYID, USUBJID) |> mutate(.ec_any = TRUE)45fa_any <- fa |> distinct(STUDYID, USUBJID) |> mutate(.fa_any = TRUE)4647adsl <- base |>48  left_join(ex_adj, by = c("STUDYID", "USUBJID")) |>49  left_join(ec_adj, by = c("STUDYID", "USUBJID")) |>50  left_join(fa_adj, by = c("STUDYID", "USUBJID")) |>51  left_join(ex_any, by = c("STUDYID", "USUBJID")) |>52  left_join(ec_any, by = c("STUDYID", "USUBJID")) |>53  left_join(fa_any, by = c("STUDYID", "USUBJID")) |>54  mutate(55    DOSADJFL = case_when(56      .ex_adj %in% TRUE | .ec_adj %in% TRUE | .fa_adj %in% TRUE ~ "Y",57      .ex_any %in% TRUE | .ec_any %in% TRUE | .fa_any %in% TRUE ~ "N"58    )59  ) |>60  select(STUDYID, USUBJID, DOSADJFL)6162dir.create("/app/output", showWarnings = FALSE)63write_csv(adsl, "/app/output/adsl.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adsl-dose-adjustment (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"121314def read_csv(name):15    path = os.path.join(INPUT_DIR, name)16    with open(path, newline="", encoding="utf-8") as f:17        return list(csv.DictReader(f))181920def filled(value):21    return value is not None and value.strip() != ""222324def main():25    subjects = read_csv("adsl.csv")26    ex = read_csv("ex.csv")27    ec = read_csv("ec.csv")28    fa = read_csv("fa.csv")2930    has_record = set()31    qualifying = set()3233    for row in ex:34        key = (row["STUDYID"], row["USUBJID"])35        has_record.add(key)36        if filled(row.get("EXADJ")):37            qualifying.add(key)3839    for row in ec:40        key = (row["STUDYID"], row["USUBJID"])41        has_record.add(key)42        if filled(row.get("ECADJ")):43            qualifying.add(key)4445    for row in fa:46        key = (row["STUDYID"], row["USUBJID"])47        has_record.add(key)48        if (49            row.get("FATESTCD") == "OCCUR"50            and row.get("FAOBJ") == "DOSE ADJUSTMENT"51            and row.get("FASTRESC") == "Y"52        ):53            qualifying.add(key)5455    os.makedirs(OUTPUT_DIR, exist_ok=True)56    out_path = os.path.join(OUTPUT_DIR, "adsl.csv")57    with open(out_path, "w", newline="", encoding="utf-8") as f:58        writer = csv.writer(f)59        writer.writerow(["STUDYID", "USUBJID", "DOSADJFL"])60        for subj in subjects:61            key = (subj["STUDYID"], subj["USUBJID"])62            if key in qualifying:63                flag = "Y"64            elif key in has_record:65                flag = "N"66            else:67                flag = ""68            writer.writerow([subj["STUDYID"], subj["USUBJID"], flag])697071if __name__ == "__main__":72    main()

1/* opensas reference solution for the yamaa benchmark adam-adsl-dose-adjustment.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data adsl;6  length STUDYID USUBJID $1024;7  infile "/app/input/adsl.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024.;9run;1011data ec;12  length STUDYID USUBJID ECADJ $1024;13  infile "/app/input/ec.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024. ECADJ : $char1024.;15run;1617data ex;18  length STUDYID USUBJID EXADJ $1024;19  infile "/app/input/ex.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;20  input STUDYID : $char1024. USUBJID : $char1024. EXADJ : $char1024.;21run;2223data fa;24  length STUDYID USUBJID FATESTCD FAOBJ FASTRESC $1024;25  infile "/app/input/fa.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;26  input STUDYID : $char1024. USUBJID : $char1024. FATESTCD : $char1024. FAOBJ : $char1024. FASTRESC : $char1024.;27run;2829proc sql;30  create table evidence as31  select STUDYID,USUBJID,case when not missing(EXADJ) then 1 else 0 end as adjusted from ex32  union all select STUDYID,USUBJID,case when not missing(ECADJ) then 1 else 0 end from ec33  union all select STUDYID,USUBJID,case when FATESTCD='OCCUR' and FAOBJ='DOSE ADJUSTMENT' and FASTRESC='Y' then 1 else 0 end from fa;34  create table flags as select STUDYID,USUBJID,max(adjusted) as adjusted,count(*) as records from evidence group by STUDYID,USUBJID;35  create table result as select a.*, case when b.adjusted=1 then 'Y' when b.records>0 then 'N' else '' end as DOSADJFL from adsl as a left join flags as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID;36quit;3738proc export data=result(keep=STUDYID USUBJID DOSADJFL) outfile="/app/output/adsl.csv" dbms=csv replace; run;