Derive BMI

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

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

1# Reference solution for the yamaa benchmark adam-advs-bmi (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)910vs <- read_csv(11  "/app/input/vs.csv",12  col_types = cols(VSSTRESN = col_double(), .default = col_character())13)14adsl <- read_csv(15  "/app/input/adsl.csv",16  col_types = cols(HEIGHTBL = col_double(), .default = col_character())17)1819# Every collected result stays in place.20collected <- vs |>21  select(STUDYID, USUBJID, AVISIT = VISIT, PARAMCD = VSTESTCD, PARAM = VSTEST, AVAL = VSSTRESN)2223# One BMI record for each weight with a result, using the subject's24# baseline height in metres. Without a usable height the record stays25# with no value.26weights <- vs |>27  filter(VSTESTCD %in% "WEIGHT", !is.na(VSSTRESN)) |>28  left_join(adsl |> select(USUBJID, HEIGHTBL), by = "USUBJID") |>29  mutate(30    BMI = if_else(31      !is.na(HEIGHTBL) & HEIGHTBL != 0,32      VSSTRESN / ((HEIGHTBL / 100) ^ 2),33      NA_real_34    )35  ) |>36  transmute(37    STUDYID, USUBJID, AVISIT = VISIT,38    PARAMCD = "BMI", PARAM = "Body Mass Index (kg/m^2)", AVAL = BMI39  )4041advs <- bind_rows(collected, weights) |>42  arrange(USUBJID, AVISIT, PARAMCD)4344dir.create("/app/output", showWarnings = FALSE)45write_csv(advs, "/app/output/advs.csv", na = "")

1# Reference solution for the yamaa benchmark adam-advs-bmi (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 csv89INPUT_DIR = "/app/input"10OUTPUT_DIR = "/app/output"1112# Baseline height (cm) per subject from ADSL.13baseline_height_cm = {}14with open(f"{INPUT_DIR}/adsl.csv", newline="") as f:15    for row in csv.DictReader(f):16        h = (row.get("HEIGHTBL") or "").strip()17        baseline_height_cm[row["USUBJID"]] = float(h) if h else None1819rows = []20with open(f"{INPUT_DIR}/vs.csv", newline="") as f:21    for rec in csv.DictReader(f):22        result = (rec.get("VSSTRESN") or "").strip()23        rows.append(24            {25                "STUDYID": rec["STUDYID"],26                "USUBJID": rec["USUBJID"],27                "AVISIT": rec["VISIT"],28                "PARAMCD": rec["VSTESTCD"],29                "PARAM": rec["VSTEST"],30                "AVAL": result,31            }32        )33        # A BMI record follows each collected weight record with a result.34        if rec["VSTESTCD"] == "WEIGHT" and result:35            height_cm = baseline_height_cm.get(rec["USUBJID"])36            if height_cm is None or height_cm == 0:37                bmi = ""38            else:39                height_m = height_cm / 100.040                bmi = repr(float(result) / (height_m * height_m))41            rows.append(42                {43                    "STUDYID": rec["STUDYID"],44                    "USUBJID": rec["USUBJID"],45                    "AVISIT": rec["VISIT"],46                    "PARAMCD": "BMI",47                    "PARAM": "Body Mass Index (kg/m^2)",48                    "AVAL": bmi,49                }50            )5152columns = ["STUDYID", "USUBJID", "AVISIT", "PARAMCD", "PARAM", "AVAL"]53with open(f"{OUTPUT_DIR}/advs.csv", "w", newline="") as f:54    writer = csv.DictWriter(f, fieldnames=columns)55    writer.writeheader()56    writer.writerows(rows)

1/* opensas reference solution for the yamaa benchmark adam-advs-bmi.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data adsl;6  length STUDYID USUBJID $1024;7  infile "/app/input/adsl.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. HEIGHTBL;9run;1011data vs;12  length STUDYID USUBJID VSTESTCD VSTEST VISIT $1024;13  infile "/app/input/vs.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024. VSSEQ VSTESTCD : $char1024. VSTEST : $char1024. VSSTRESN VISIT : $char1024.;15run;1617proc sql; create table joined as select a.*,b.HEIGHTBL from vs as a left join adsl as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID; quit;18data result;19  length AVISIT $1024 PARAMCD $16 PARAM $1024;20  set joined;21  AVISIT=VISIT; PARAMCD=VSTESTCD; PARAM=VSTEST; AVAL=VSSTRESN; output;22  if VSTESTCD='WEIGHT' and not missing(VSSTRESN) then do;23    PARAMCD='BMI'; PARAM='Body Mass Index (kg/m^2)'; AVAL=.;24    if not missing(HEIGHTBL) and HEIGHTBL ne 0 then AVAL=VSSTRESN/(HEIGHTBL/100)**2;25    output;26  end;27run;2829proc sql;30  create table final as select STUDYID, USUBJID, AVISIT, PARAMCD, PARAM, AVAL from result;31quit;32proc export data=final outfile="/app/output/advs.csv" dbms=csv replace; run;