Standardize Vital-Signs Units

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

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

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 1.67"""Build the SDTM VS dataset from VS_RAW with unit standardization.89Reads /app/input/vs_raw.csv and writes /app/output/vs.csv with one10record per collected vital-signs measurement. Standard units: cm for11height, kg for weight, C for temperature.12"""1314import csv15import os1617INPUT_DIR = "/app/input"18OUTPUT_DIR = "/app/output"1920STANDARD_UNIT = {"HEIGHT": "cm", "WEIGHT": "kg", "TEMP": "C"}21LB_TO_KG = 0.453592372223COLUMNS = [24    "DOMAIN", "STUDYID", "USUBJID", "VSSEQ", "VISIT", "VSTESTCD",25    "VSTEST", "VSORRES", "VSORRESU", "VSSTRESN", "VSSTRESC",26    "VSSTRESU", "VSSTAT",27]282930def format_number(value):31    """Write a number as text, dropping trailing zeros (72.50 -> 72.5)."""32    rounded = round(value, 10)33    if rounded == int(rounded):34        return str(int(rounded))35    return repr(rounded)363738def standardize(testcd, value, unit):39    """Return the result as a number in the test's standard unit."""40    if testcd == "WEIGHT" and unit == "LB":41        return value * LB_TO_KG42    if testcd == "TEMP" and unit == "F":43        return (value - 32) * 5 / 944    return value454647def main():48    with open(os.path.join(INPUT_DIR, "vs_raw.csv"), newline="") as f:49        rows = list(csv.DictReader(f))5051    out_rows = []52    for row in rows:53        collected = row["VSORRES"].strip()54        testcd = row["VSTESTCD"]55        if collected:56            value = float(collected)57            std_value = standardize(testcd, value, row["VSORRESU"])58            orres = format_number(value)59            orresu = row["VSORRESU"]60            stresn = format_number(std_value)61            stresc = stresn62            stresu = STANDARD_UNIT[testcd]63            stat = ""64        else:65            orres = ""66            orresu = ""67            stresn = ""68            stresc = ""69            stresu = ""70            stat = "NOT DONE"71        out_rows.append({72            "DOMAIN": "VS",73            "STUDYID": row["STUDYID"],74            "USUBJID": row["USUBJID"],75            "VSSEQ": row["VSSEQ"],76            "VISIT": row["VISIT"],77            "VSTESTCD": testcd,78            "VSTEST": row["VSTEST"],79            "VSORRES": orres,80            "VSORRESU": orresu,81            "VSSTRESN": stresn,82            "VSSTRESC": stresc,83            "VSSTRESU": stresu,84            "VSSTAT": stat,85        })8687    os.makedirs(OUTPUT_DIR, exist_ok=True)88    with open(os.path.join(OUTPUT_DIR, "vs.csv"), "w", newline="") as f:89        writer = csv.DictWriter(f, fieldnames=COLUMNS)90        writer.writeheader()91        writer.writerows(out_rows)929394if __name__ == "__main__":95    main()

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;