Apply the stated policy to qualified laboratory results

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

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

1# Reference solution for the yamaa benchmark adam-adlb-limit-imputation (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)910lb <- read_csv(11  "/app/input/lb.csv",12  col_types = cols(13    LBSEQ = col_integer(),14    .default = col_character()15  ),16  na = ""17)1819# The numeric boundary of the reported result: the decimal number after an20# optional "<", ">", "<=", ">=" or "=" prefix. It has no value when no21# result was reported.22based <- lb |>23  mutate(24    PARAMCD = LBTESTCD,25    AVALC = LBSTRESC,26    AVALU = LBSTRESU,27    LIMITVAL = as.numeric(sub("^[<>=]+", "", AVALC))28  )2930# Only a strict inequality receives the one-unit offset; an inclusive31# limit, an ordinary number and an "=" result keep the number itself.32adlb <- based |>33  mutate(34    AVAL = case_when(35      !is.na(AVALC) & startsWith(AVALC, "<") & !startsWith(AVALC, "<=") ~36        LIMITVAL - 1,37      !is.na(AVALC) & startsWith(AVALC, ">") & !startsWith(AVALC, ">=") ~38        LIMITVAL + 1,39      .default = LIMITVAL40    ),41    DTYPE = if_else(42      !is.na(AVALC) & (startsWith(AVALC, "<") | startsWith(AVALC, ">")),43      "IMPUTATION",44      NA_character_45    )46  ) |>47  select(48    STUDYID, USUBJID, LBSEQ, PARAMCD, AVALC, AVAL, AVALU, DTYPE49  )5051dir.create("/app/output", showWarnings = FALSE)52write_csv(adlb, "/app/output/adlb.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adlb-limit-imputation (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 csv8910def fmt(value):11    if value == int(value):12        return str(int(value))13    return repr(value)141516def derive(text):17    """Return (AVAL text, DTYPE text) for a reported result string."""18    if text is None or text.strip() == "":19        return "", ""20    t = text.strip()21    for prefix, kind in (("<=", "le"), (">=", "ge"), ("<", "lt"), (">", "gt"), ("=", "eq")):22        if t.startswith(prefix):23            limit = float(t[len(prefix):])24            if kind == "lt":25                return fmt(limit - 1), "IMPUTATION"26            if kind == "gt":27                return fmt(limit + 1), "IMPUTATION"28            if kind in ("le", "ge"):29                return fmt(limit), "IMPUTATION"30            return fmt(limit), ""31    return fmt(float(t)), ""323334def main():35    with open("/app/input/lb.csv", newline="") as f:36        rows = list(csv.DictReader(f))37    out = []38    for r in rows:39        aval, dtype = derive(r["LBSTRESC"])40        out.append({41            "STUDYID": r["STUDYID"],42            "USUBJID": r["USUBJID"],43            "LBSEQ": r["LBSEQ"],44            "PARAMCD": r["LBTESTCD"],45            "AVALC": r["LBSTRESC"],46            "AVAL": aval,47            "AVALU": r["LBSTRESU"],48            "DTYPE": dtype,49        })50    fields = ["STUDYID", "USUBJID", "LBSEQ", "PARAMCD", "AVALC", "AVAL", "AVALU", "DTYPE"]51    with open("/app/output/adlb.csv", "w", newline="") as f:52        w = csv.DictWriter(f, fieldnames=fields)53        w.writeheader()54        w.writerows(out)555657if __name__ == "__main__":58    main()

1/* opensas reference solution for the yamaa benchmark adam-adlb-limit-imputation.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data lb;6  length STUDYID USUBJID LBTESTCD LBSTRESC LBSTRESU $1024;7  infile "/app/input/lb.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. LBSEQ LBTESTCD : $char1024. LBSTRESC : $char1024. LBSTRESU : $char1024.;9run;1011data result;12  length DTYPE $1024;13  set lb;14  PARAMCD = LBTESTCD;15  AVALC = LBSTRESC;16  AVALU = LBSTRESU;17  /* The numeric boundary: the number after any inequality or "=" prefix. */18  NUMTXT = AVALC;19  if substr(NUMTXT, 1, 2) in ('<=', '>=') then NUMTXT = substr(NUMTXT, 3);20  else if substr(NUMTXT, 1, 1) in ('<', '>', '=') then NUMTXT = substr(NUMTXT, 2);21  if NUMTXT ne '' then LIMITVAL = input(NUMTXT, best32.);22  else LIMITVAL = .;23  /* Only a strict inequality receives the one-unit offset. */24  if missing(AVALC) then AVAL = .;25  else if substr(AVALC, 1, 2) in ('<=', '>=') then AVAL = LIMITVAL;26  else if substr(AVALC, 1, 1) = '<' then AVAL = LIMITVAL - 1;27  else if substr(AVALC, 1, 1) = '>' then AVAL = LIMITVAL + 1;28  else AVAL = LIMITVAL;29  if substr(AVALC, 1, 1) in ('<', '>') then DTYPE = 'IMPUTATION';30  else DTYPE = '';31  drop NUMTXT LIMITVAL;32run;3334proc sql;35  create table final as select STUDYID, USUBJID, LBSEQ, PARAMCD, AVALC, AVAL, AVALU, DTYPE from result;36quit;37proc export data=final outfile="/app/output/adlb.csv" dbms=csv replace; run;