CTCAE v5.0 Grading

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

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

1# Reference solution for the yamaa benchmark sdtm-lb-grading (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)910raw <- read_csv(11  "/app/input/lb_raw.csv",12  col_types = cols(13    LBSEQ = col_integer(),14    LBSTRESN = col_double(),15    .default = col_character()16  )17)1819toxgrade <- function(test, sex, value) {20  if (is.na(value)) return(NA_character_)21  if (test == "ANC") {22    if (value < 0.5) return("4")23    if (value < 1.0) return("3")24    if (value < 1.5) return("2")25    if (value < 1.8) return("1")26    return("0")27  }28  if (test == "HGB") {29    if (!sex %in% c("M", "F")) return(NA_character_)30    if (value < 8.0) return("3")31    if (value < 10.0) return("2")32    limit <- if (sex == "M") 13.5 else 12.033    if (value < limit) return("1")34    return("0")35  }36  NA_character_37}3839lb <- raw |>40  filter(LBTESTCD %in% c("ANC", "HGB"), !(LBTESTCD == "HGB" & !SEX %in% c("M", "F"))) |>41  rowwise() |>42  mutate(LBTOXGR = toxgrade(LBTESTCD, SEX, LBSTRESN)) |>43  ungroup() |>44  mutate(DOMAIN = "LB") |>45  select(DOMAIN, STUDYID, USUBJID, LBSEQ, LBTESTCD, LBSTRESN, LBTOXGR) |>46  arrange(STUDYID, USUBJID, LBSEQ)4748dir.create("/app/output", showWarnings = FALSE)49write_csv(lb, "/app/output/lb.csv", na = "")

1# Reference solution for the yamaa benchmark sdtm-lb-grading (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 LB dataset from LB_RAW.89One record per collected neutrophil (ANC) or hemoglobin (HGB) result,10with LBTOXGR the standard toxicity grade from the band set for the11test (and, for hemoglobin, the sex). Each band includes its lower12limit and excludes its upper one. Results for any other test, and13hemoglobin results with a sex other than "M" or "F", get no record.14"""1516import csv17import os1819INPUT_DIR = "/app/input"20OUTPUT_DIR = "/app/output"2122# (lower limit inclusive, grade) pairs in ascending order; a value23# takes the grade of the last band whose lower limit it reaches.24ANC_BANDS = [(0.0, "4"), (0.5, "3"), (1.0, "2"), (1.5, "1"), (1.8, "0")]25HGB_BANDS = {26    "M": [(0.0, "3"), (8.0, "2"), (10.0, "1"), (13.5, "0")],27    "F": [(0.0, "3"), (8.0, "2"), (10.0, "1"), (12.0, "0")],28}293031def grade(value, bands):32    result = None33    for lower, band_grade in bands:34        if value >= lower:35            result = band_grade36    return result373839def main():40    with open(os.path.join(INPUT_DIR, "lb_raw.csv"), newline="") as f:41        rows = list(csv.DictReader(f))4243    out = []44    for row in rows:45        test = row["LBTESTCD"]46        value = float(row["LBSTRESN"])47        if test == "ANC":48            toxgr = grade(value, ANC_BANDS)49        elif test == "HGB":50            bands = HGB_BANDS.get(row["SEX"])51            if bands is None:52                continue53            toxgr = grade(value, bands)54        else:55            continue56        out.append(57            {58                "DOMAIN": "LB",59                "STUDYID": row["STUDYID"],60                "USUBJID": row["USUBJID"],61                "LBSEQ": row["LBSEQ"],62                "LBTESTCD": test,63                "LBSTRESN": row["LBSTRESN"],64                "LBTOXGR": toxgr,65            }66        )6768    os.makedirs(OUTPUT_DIR, exist_ok=True)69    columns = [70        "DOMAIN",71        "STUDYID",72        "USUBJID",73        "LBSEQ",74        "LBTESTCD",75        "LBSTRESN",76        "LBTOXGR",77    ]78    with open(os.path.join(OUTPUT_DIR, "lb.csv"), "w", newline="") as f:79        writer = csv.DictWriter(f, fieldnames=columns)80        writer.writeheader()81        writer.writerows(out)828384if __name__ == "__main__":85    main()

1/* opensas reference solution for the yamaa benchmark sdtm-lb-grading.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data lb_raw;6  length STUDYID USUBJID LBTESTCD SEX REPROGRADE $1024;7  infile "/app/input/lb_raw.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. LBSEQ LBTESTCD : $char1024. SEX : $char1024. LBSTRESN REPROGRADE : $char1024.;9run;1011data result; set lb_raw; length DOMAIN $2; DOMAIN='LB'; LBTOXGR=.;12if LBTESTCD='ANC' then do; if missing(LBSTRESN) then LBTOXGR=.; else if LBSTRESN<0.5 then LBTOXGR=4; else if LBSTRESN<1 then LBTOXGR=3; else if LBSTRESN<1.5 then LBTOXGR=2; else if LBSTRESN<1.8 then LBTOXGR=1; else LBTOXGR=0; end;13else if LBTESTCD='HGB' and SEX in ('M','F') then do; if missing(LBSTRESN) then LBTOXGR=.; else if LBSTRESN<8 then LBTOXGR=3; else if LBSTRESN<10 then LBTOXGR=2; else if (SEX='M' and LBSTRESN<13.5) or (SEX='F' and LBSTRESN<12) then LBTOXGR=1; else LBTOXGR=0; end; else delete; run;14proc sql;15  create table final as select DOMAIN, STUDYID, USUBJID, LBSEQ, LBTESTCD, LBSTRESN, LBTOXGR from result;16quit;17proc export data=final outfile="/app/output/lb.csv" dbms=csv replace; run;