Assign Analysis Windows from the Window Table

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

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

1# Reference solution for the yamaa benchmark adam-advs-window-table (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(purrr)9library(readr)1011raw <- read_csv(12  "/app/input/advs_raw.csv",13  col_types = cols(14    VSSEQ = col_integer(), ADT = col_date(), ADY = col_integer(),15    AVAL = col_double(), .default = col_character()16  )17)18windows <- read_csv(19  "/app/input/awindow.csv",20  col_types = cols(21    AVISITN = col_integer(), AWLO = col_integer(), AWHI = col_integer(),22    AWTARGET = col_integer(), .default = col_character()23  )24)2526# The one window in the same study whose first-to-last range, both ends27# inclusive, holds the study day. An absent bound never matches.28match_window <- function(studyid, ady) {29  if (is.na(ady)) {30    return(tibble::tibble(AVISIT = NA_character_, AVISITN = NA_integer_, AWTARGET = NA_integer_))31  }32  hit <- windows |>33    filter(34      STUDYID == studyid, !is.na(AWLO), !is.na(AWHI),35      AWLO <= ady, ady <= AWHI36    ) |>37    slice_head(n = 1)38  if (nrow(hit) == 0) {39    tibble::tibble(AVISIT = NA_character_, AVISITN = NA_integer_, AWTARGET = NA_integer_)40  } else {41    hit |> select(AVISIT, AVISITN, AWTARGET)42  }43}4445framed <- raw |>46  arrange(STUDYID, USUBJID, VSSEQ) |>47  mutate(window = map2(STUDYID, ADY, match_window)) |>48  tidyr::unnest(window) |>49  mutate(50    AWTDIFF = ADY - AWTARGET,51    AWTABS = abs(AWTDIFF)52  )5354# The record nearest its target in each study, subject, parameter, and55# visit; the lower sequence number breaks a tie.56flagged <- framed |>57  filter(!is.na(AVISIT)) |>58  arrange(AWTABS, VSSEQ) |>59  distinct(STUDYID, USUBJID, PARAMCD, AVISIT, .keep_all = TRUE) |>60  select(STUDYID, USUBJID, PARAMCD, AVISIT, VSSEQ) |>61  mutate(ANL01FL = "Y")6263advs <- framed |>64  select(-AWTABS) |>65  left_join(flagged, by = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT", "VSSEQ")) |>66  arrange(STUDYID, USUBJID, VSSEQ) |>67  select(68    STUDYID, USUBJID, PARAMCD, VSSEQ, VISIT, ADT, ADY, AVAL,69    AVISIT, AVISITN, AWTARGET, AWTDIFF, ANL01FL70  )7172dir.create("/app/output", showWarnings = FALSE)73write_csv(advs, "/app/output/advs.csv", na = "")

1# Reference solution for the yamaa benchmark adam-advs-window-table (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 csv89INPUT_DIR = "/app/input"10OUTPUT_DIR = "/app/output"111213def read_csv(path):14    with open(path, newline="") as f:15        return list(csv.DictReader(f))161718def to_int(text):19    if text is None or text.strip() == "":20        return None21    return int(text)222324def main():25    raw = read_csv(f"{INPUT_DIR}/advs_raw.csv")26    windows = read_csv(f"{INPUT_DIR}/awindow.csv")2728    windows_by_study = {}29    for w in windows:30        windows_by_study.setdefault(w["STUDYID"], []).append(w)3132    records = []33    for row in raw:34        ady = to_int(row["ADY"])35        matched = None36        if ady is not None:37            for w in windows_by_study.get(row["STUDYID"], []):38                lo = to_int(w["AWLO"])39                hi = to_int(w["AWHI"])40                # An absent bound is not an open-ended one: a window41                # whose last day was never stated matches nothing.42                if lo is None or hi is None:43                    continue44                if lo <= ady <= hi:45                    matched = w46                    break4748        rec = {49            "STUDYID": row["STUDYID"],50            "USUBJID": row["USUBJID"],51            "PARAMCD": row["PARAMCD"],52            "VSSEQ": row["VSSEQ"],53            "VISIT": row["VISIT"],54            "ADT": row["ADT"],55            "ADY": row["ADY"],56            "AVAL": row["AVAL"],57            "AVISIT": "",58            "AVISITN": "",59            "AWTARGET": "",60            "AWTDIFF": "",61            "ANL01FL": "",62        }63        diff = None64        if matched is not None:65            target = to_int(matched["AWTARGET"])66            rec["AVISIT"] = matched["AVISIT"]67            rec["AVISITN"] = matched["AVISITN"]68            rec["AWTARGET"] = matched["AWTARGET"]69            if target is not None:70                diff = ady - target71                rec["AWTDIFF"] = str(diff)72        rec["_diff"] = diff73        records.append(rec)7475    # ANL01FL is Y on the record nearest its window target among the76    # records for the same study, subject, parameter and analysis77    # visit; the lower VSSEQ breaks a tie.78    groups = {}79    for rec in records:80        if rec["AVISIT"] == "" or rec["_diff"] is None:81            continue82        key = (rec["STUDYID"], rec["USUBJID"], rec["PARAMCD"], rec["AVISIT"])83        groups.setdefault(key, []).append(rec)84    for group in groups.values():85        best = min(group, key=lambda r: (abs(r["_diff"]), int(r["VSSEQ"])))86        best["ANL01FL"] = "Y"8788    fieldnames = [89        "STUDYID", "USUBJID", "PARAMCD", "VSSEQ", "VISIT", "ADT", "ADY",90        "AVAL", "AVISIT", "AVISITN", "AWTARGET", "AWTDIFF", "ANL01FL",91    ]92    with open(f"{OUTPUT_DIR}/advs.csv", "w", newline="") as f:93        writer = csv.DictWriter(f, fieldnames=fieldnames)94        writer.writeheader()95        for rec in records:96            writer.writerow({k: rec[k] for k in fieldnames})979899if __name__ == "__main__":100    main()

1/* opensas reference solution for the yamaa benchmark adam-advs-window-table.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data advs_raw;6  length STUDYID USUBJID PARAMCD VISIT ADT $1024;7  infile "/app/input/advs_raw.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. PARAMCD : $char1024. VSSEQ VISIT : $char1024. VISITNUM ADT : $char1024. ADY AVAL;9run;1011data awindow;12  length STUDYID AVISIT $1024;13  infile "/app/input/awindow.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. AVISIT : $char1024. AVISITN AWLO AWHI AWTARGET;15run;1617proc sql;18  create table candidates as select a.*,b.AVISIT,b.AVISITN,b.AWTARGET,a.ADY-b.AWTARGET as AWTDIFF from advs_raw as a left join awindow as b19    on a.STUDYID=b.STUDYID and not missing(a.ADY) and not missing(b.AWLO) and not missing(b.AWHI) and a.ADY>=b.AWLO and a.ADY<=b.AWHI;20quit;21data ordered; set candidates; distance=abs(AWTDIFF); nodistance=missing(distance); run;22proc sort data=ordered; by STUDYID USUBJID PARAMCD AVISITN nodistance distance VSSEQ; run;23data result; length ANL01FL $1; set ordered; by STUDYID USUBJID PARAMCD AVISITN; if first.AVISITN and not missing(AVISITN) then ANL01FL='Y'; run;2425proc sql;26  create table final as select STUDYID, USUBJID, PARAMCD, VSSEQ, VISIT, ADT, ADY, AVAL, AVISIT, AVISITN, AWTARGET, AWTDIFF, ANL01FL from result;27quit;28proc export data=final outfile="/app/output/advs.csv" dbms=csv replace; run;