Standardize Vital-Signs Units

1library(yamaa)23vs <- yamaa_domain("spec.yaml")$output4vs

1import yamaa23vs = yamaa.yamaa_domain("spec.yaml").output4vs

1# Reference solution for the yamaa benchmark sdtm-vs-units (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)910fmt_text <- function(x) {11  if (is.na(x)) {12    return(NA_character_)13  }14  if (x == floor(x)) {15    formatC(x, format = "f", digits = 0)16  } else {17    format(x, scientific = FALSE, trim = TRUE, digits = 15)18  }19}2021fmt_orres <- function(x) {22  if (is.na(x) || x == "") {23    return(NA_character_)24  }25  num <- suppressWarnings(as.numeric(x))26  if (is.na(num)) {27    return(x)28  }29  fmt_text(num)30}3132raw <- read_csv(33  "/app/input/vs_raw.csv",34  col_types = cols(VSSEQ = col_integer(), .default = col_character())35)3637vs <- raw |>38  mutate(39    has_result = !is.na(VSORRES) & VSORRES != "",40    VSORRES = vapply(VSORRES, fmt_orres, character(1)),41    value = suppressWarnings(as.numeric(raw$VSORRES)),42    VSSTRESN = case_when(43      !has_result ~ NA_real_,44      VSTESTCD == "HEIGHT" ~ value,45      VSTESTCD == "WEIGHT" & VSORRESU == "LB" ~ value * 0.45359237,46      VSTESTCD == "WEIGHT" ~ value,47      VSORRESU == "F" ~ (value - 32) * 5 / 9,48      .default = value49    ),50    VSSTRESC = vapply(VSSTRESN, fmt_text, character(1)),51    VSSTRESU = case_when(52      !has_result ~ NA_character_,53      VSTESTCD == "HEIGHT" ~ "cm",54      VSTESTCD == "WEIGHT" ~ "kg",55      .default = "C"56    ),57    VSORRESU = if_else(has_result, VSORRESU, NA_character_),58    VSSTAT = if_else(has_result, NA_character_, "NOT DONE"),59    DOMAIN = "VS",60    test_ord = case_when(61      VSTESTCD == "HEIGHT" ~ 1L,62      VSTESTCD == "WEIGHT" ~ 2L,63      .default = 3L64    )65  ) |>66  arrange(test_ord, USUBJID, VSSEQ) |>67  select(68    DOMAIN, STUDYID, USUBJID, VSSEQ, VISIT, VSTESTCD, VSTEST, VSORRES,69    VSORRESU, VSSTRESN, VSSTRESC, VSSTRESU, VSSTAT70  )7172dir.create("/app/output", showWarnings = FALSE)73write_csv(vs, "/app/output/vs.csv", na = "")

1# Reference solution for the yamaa benchmark sdtm-vs-units (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 1.67from pathlib import Path89import polars as pl101112def fmt_text(x: float | None) -> str | None:13    if x is None:14        return None15    import math1617    if isinstance(x, float) and (math.isnan(x) or math.isinf(x)):18        return None19    fx = float(x)20    if fx.is_integer():21        return str(int(fx))22    text = f"{fx:.15g}"23    return text242526def fmt_orres(x: str | None) -> str | None:27    if x is None or x == "":28        return None29    try:30        return fmt_text(float(x))31    except ValueError:32        return x333435raw = pl.read_csv("/app/input/vs_raw.csv", infer_schema=False).with_columns(36    pl.col("VSSEQ").cast(pl.Int64),37)3839rows = raw.to_dicts()40for row in rows:41    orres = row["VSORRES"]42    has_result = orres is not None and orres != ""43    test = row["VSTESTCD"]44    unit = row["VSORRESU"]45    if not has_result:46        row["VSORRES"] = None47        row["VSORRESU"] = None48        row["VSSTRESN"] = None49        row["VSSTRESC"] = None50        row["VSSTRESU"] = None51        row["VSSTAT"] = "NOT DONE"52        continue53    row["VSORRES"] = fmt_orres(orres)54    value = float(orres)55    if test == "HEIGHT":56        std = value57        std_unit = "cm"58    elif test == "WEIGHT":59        std = value * 0.45359237 if unit == "LB" else value60        std_unit = "kg"61    else:62        std = (value - 32) * 5 / 9 if unit == "F" else value63        std_unit = "C"64    row["VSSTRESN"] = std65    row["VSSTRESC"] = fmt_text(std)66    row["VSSTRESU"] = std_unit67    # Original unit is empty when no result was collected; otherwise as68    # collected.69    row["VSORRESU"] = unit70    row["VSSTAT"] = None7172vs = (73    pl.DataFrame(rows)74    .with_columns(75        DOMAIN=pl.lit("VS"),76        _ord=pl.col("VSTESTCD").replace_strict(77            {"HEIGHT": 1, "WEIGHT": 2, "TEMP": 3},78            default=9,79            return_dtype=pl.Int64,80        ),81    )82    .sort(["_ord", "USUBJID", "VSSEQ"])83    .select(84        "DOMAIN",85        "STUDYID",86        "USUBJID",87        "VSSEQ",88        "VISIT",89        "VSTESTCD",90        "VSTEST",91        "VSORRES",92        "VSORRESU",93        "VSSTRESN",94        "VSSTRESC",95        "VSSTRESU",96        "VSSTAT",97    )98)99100Path("/app/output").mkdir(exist_ok=True)101vs.write_csv("/app/output/vs.csv")

1/* opensas reference solution for the yamaa benchmark sdtm-vs-units.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data vs_raw;6  length STUDYID USUBJID VISIT VSTESTCD VSTEST VSORRES VSORRESU $1024;7  infile "/app/input/vs_raw.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. VSSEQ VISIT : $char1024. VSTESTCD : $char1024. VSTEST : $char1024. VSORRES : $char1024. VSORRESU : $char1024.;9run;1011data result; set vs_raw; length DOMAIN $2 VSSTRESC VSSTRESU VSSTAT $1024; DOMAIN='VS'; VSSTRESN=.; VSSTRESC=''; VSSTRESU=''; VSSTAT='';12if missing(VSORRES) then do; VSSTAT='NOT DONE'; VSORRESU=''; end;13else do; VALUE=input(VSORRES,best32.); VSORRES=strip(put(VALUE,best15.)); VSSTRESN=VALUE;14if VSTESTCD='HEIGHT' then VSSTRESU='cm'; else if VSTESTCD='WEIGHT' then do; VSSTRESU='kg'; if VSORRESU='LB' then VSSTRESN=VALUE*0.45359237; end;15else do; VSSTRESU='C'; if VSORRESU='F' then VSSTRESN=(VALUE-32)*5/9; end;16/* Fifteen significant digits; field width alone counts the decimal point.17   Explicit decimal precision avoids BEST32 exposing binary rounding noise. */18if VSSTRESN=0 then VSSTRESC='0';19else do;20  DECIMALS=max(0,14-floor(log10(abs(VSSTRESN))));21  VSSTRESC=strip(putn(VSSTRESN,cats('32.',put(DECIMALS,best12.))));22  if index(VSSTRESC,'.')>0 then do;23    VSSTRESC=prxchange('s/0+$//',1,VSSTRESC);24    VSSTRESC=prxchange('s/\.$//',1,VSSTRESC);25  end;26end;27end; run;28proc sql;29  create table final as select DOMAIN, STUDYID, USUBJID, VSSEQ, VISIT, VSTESTCD, VSTEST, VSORRES, VSORRESU, VSSTRESN, VSSTRESC, VSSTRESU, VSSTAT from result;30quit;31proc export data=final outfile="/app/output/vs.csv" dbms=csv replace; run;