Assign a Composite Responder Status

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

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

1# Reference solution for the yamaa benchmark adam-adrs-composite-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)910adsl <- read_csv(11  "/app/input/adsl.csv",12  col_types = cols(.default = col_character())13)14raw <- read_csv(15  "/app/input/adrs_raw.csv",16  col_types = cols(PCHG = col_double(), .default = col_character())17)1819# The checks apply in a fixed order: a safety or discontinuation rule20# first, then a missing component, then the 75% reduction threshold.21adrs <- raw |>22  left_join(select(adsl, USUBJID, SAEFL, DCSREAS), by = "USUBJID") |>23  mutate(24    PARAMCD = "RESP75",25    PARAM = "EASI-75 Response",26    safety = SAEFL %in% "Y" | (!is.na(DCSREAS) & DCSREAS != ""),27    AVALC = case_when(28      safety ~ "NON-RESPONDER",29      is.na(PCHG) ~ "NOT EVALUABLE",30      PCHG <= -75 ~ "RESPONDER",31      .default = "NON-RESPONDER"32    ),33    ARSN = case_when(34      safety ~ "SAFETY OR DISCONTINUATION RULE",35      is.na(PCHG) ~ "COMPONENT MISSING",36      PCHG <= -75 ~ "THRESHOLD MET",37      .default = "THRESHOLD NOT MET"38    ),39    AVAL = case_when(40      AVALC == "RESPONDER" ~ 1L,41      AVALC == "NON-RESPONDER" ~ 0L42    )43  ) |>44  select(45    STUDYID, USUBJID, PARAMCD, PARAM, AVISIT, PCHG, SAEFL, DCSREAS,46    AVALC, ARSN, AVAL47  ) |>48  arrange(USUBJID, AVISIT)4950dir.create("/app/output", showWarnings = FALSE)51write_csv(adrs, "/app/output/adrs.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adrs-composite-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 1.67"""Create ADRS (EASI-75 composite response) from ADRS_RAW and ADSL.89One record per subject and analysis visit from ADRS_RAW, enriched with the10subject-level SAEFL and DCSREAS from ADSL. A subject flagged by the safety11or discontinuation rule is a non-responder whatever the percent change;12otherwise a missing percent change is not evaluable, a percent change of13-75 or less is a responder, and anything else is a non-responder.14"""1516import csv17import os1819INPUT_DIR = "/app/input"20OUTPUT_DIR = "/app/output"212223def read_csv(path):24    with open(path, newline="", encoding="utf-8") as handle:25        return list(csv.DictReader(handle))262728def main():29    raw = read_csv(os.path.join(INPUT_DIR, "adrs_raw.csv"))30    adsl = read_csv(os.path.join(INPUT_DIR, "adsl.csv"))3132    subjects = {}33    for row in adsl:34        subjects[(row["STUDYID"], row["USUBJID"])] = row3536    out_rows = []37    for row in raw:38        key = (row["STUDYID"], row["USUBJID"])39        subject = subjects.get(key, {})40        saefl = subject.get("SAEFL", "") or ""41        dcsreas = subject.get("DCSREAS", "") or ""4243        pchg_text = row["PCHG"]44        pchg = None45        if pchg_text is not None and pchg_text.strip() != "":46            pchg = float(pchg_text)4748        if saefl == "Y" or dcsreas != "":49            avalc = "NON-RESPONDER"50            arsn = "SAFETY OR DISCONTINUATION RULE"51        elif pchg is None:52            avalc = "NOT EVALUABLE"53            arsn = "COMPONENT MISSING"54        elif pchg <= -75:55            avalc = "RESPONDER"56            arsn = "THRESHOLD MET"57        else:58            avalc = "NON-RESPONDER"59            arsn = "THRESHOLD NOT MET"6061        if avalc == "RESPONDER":62            aval = "1"63        elif avalc == "NON-RESPONDER":64            aval = "0"65        else:66            aval = ""6768        out_rows.append(69            {70                "STUDYID": row["STUDYID"],71                "USUBJID": row["USUBJID"],72                "PARAMCD": "RESP75",73                "PARAM": "EASI-75 Response",74                "AVISIT": row["AVISIT"],75                "PCHG": pchg_text,76                "SAEFL": saefl,77                "DCSREAS": dcsreas,78                "AVALC": avalc,79                "ARSN": arsn,80                "AVAL": aval,81            }82        )8384    fieldnames = [85        "STUDYID",86        "USUBJID",87        "PARAMCD",88        "PARAM",89        "AVISIT",90        "PCHG",91        "SAEFL",92        "DCSREAS",93        "AVALC",94        "ARSN",95        "AVAL",96    ]97    os.makedirs(OUTPUT_DIR, exist_ok=True)98    with open(99        os.path.join(OUTPUT_DIR, "adrs.csv"), "w", newline="", encoding="utf-8"100    ) as handle:101        writer = csv.DictWriter(handle, fieldnames=fieldnames)102        writer.writeheader()103        writer.writerows(out_rows)104105106if __name__ == "__main__":107    main()

1/* opensas reference solution for the yamaa benchmark adam-adrs-composite-response.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data adrs_raw;6  length STUDYID USUBJID PARAMCD AVISIT $1024;7  infile "/app/input/adrs_raw.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. PARAMCD : $char1024. AVISIT : $char1024. PCHG;9run;1011data adsl;12  length STUDYID USUBJID SAEFL DCSREAS $1024;13  infile "/app/input/adsl.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024. SAEFL : $char1024. DCSREAS : $char1024.;15run;1617proc sql; create table joined as select a.*,b.SAEFL,b.DCSREAS from adrs_raw as a left join adsl as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID; quit;18data result;19  length PARAM $40 AVALC $20 ARSN $40;20  set joined; PARAMCD='RESP75'; PARAM='EASI-75 Response';21  if SAEFL='Y' or not missing(DCSREAS) then do; AVALC='NON-RESPONDER'; ARSN='SAFETY OR DISCONTINUATION RULE'; AVAL=0; end;22  else if missing(PCHG) then do; AVALC='NOT EVALUABLE'; ARSN='COMPONENT MISSING'; end;23  else if PCHG<=-75 then do; AVALC='RESPONDER'; ARSN='THRESHOLD MET'; AVAL=1; end;24  else do; AVALC='NON-RESPONDER'; ARSN='THRESHOLD NOT MET'; AVAL=0; end;25run;2627proc sql;28  create table final as select STUDYID, USUBJID, PARAMCD, PARAM, AVISIT, PCHG, SAEFL, DCSREAS, AVALC, ARSN, AVAL from result;29quit;30proc export data=final outfile="/app/output/adrs.csv" dbms=csv replace; run;