Infusion duration from the collected duration or the start and end times

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

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

1# Reference solution for the yamaa benchmark adam-adex-infusion-duration (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(lubridate, warn.conflicts = FALSE)9library(readr)10library(stringr)1112ex <- read_csv(13  "/app/input/ex.csv",14  col_types = cols(EXSEQ = col_integer(), .default = col_character())15)1617# A date alone has no time of day, and none is assumed; a time without18# seconds counts as second zero.19moment <- function(x) {20  full <- if_else(nchar(x) == 16, paste0(x, ":00"), x)21  if_else(!is.na(x) & nchar(x) > 10, ymd_hms(full, tz = "UTC", quiet = TRUE), as.POSIXct(NA, tz = "UTC"))22}2324# An ISO 8601 duration of days, hours, minutes and seconds, with at least one25# part; anything else counts as not collected.26collected_minutes <- function(x) {27  pattern <- "^P(?:(\\d+)D)?(?:T(?:(\\d+)H)?(?:(\\d+)M)?(?:(\\d+(?:\\.\\d+)?)S)?)?$"28  parts <- str_match(x, pattern)29  number <- function(i) coalesce(as.numeric(parts[, i]), 0)30  found <- !is.na(parts[, 1]) & rowSums(!is.na(parts[, 2:5, drop = FALSE])) > 0 & !str_ends(coalesce(x, ""), "T")31  if_else(found, number(2) * 1440 + number(3) * 60 + number(4) + number(5) / 60, NA_real_)32}3334adex <- ex |>35  mutate(36    CALCDUR = as.numeric(difftime(moment(EXENDTC), moment(EXSTDTC), units = "mins")),37    AVAL = coalesce(collected_minutes(EXDUR), CALCDUR),38    PARAMCD = "INFDUR",39    PARAM = "Infusion Duration (min)"40  ) |>41  select(STUDYID, USUBJID, EXSEQ, EXSTDTC, EXENDTC, EXDUR, PARAMCD, PARAM, AVAL, CALCDUR)4243dir.create("/app/output", showWarnings = FALSE)44write_csv(adex, "/app/output/adex.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adex-infusion-duration (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"""Create ADEX (one record per infusion) from EX.89PARAMCD is "INFDUR" and PARAM is "Infusion Duration (min)" on every10record.1112CALCDUR is the elapsed time in minutes from EXSTDTC to EXENDTC, with13seconds kept as a fraction of a minute and nothing added or rounded.14It has no value when EXSTDTC or EXENDTC was collected as a date15without a time of day.1617AVAL is the collected duration in minutes when EXDUR holds a readable18fixed-length ISO 8601 duration; otherwise AVAL is CALCDUR. Text that19is not such a duration (for example one without its leading P) counts20as not collected, and a readable collected duration always wins even21when it disagrees with the start and end times. AVAL has no value when22neither gives a value; every infusion keeps its record.23"""2425import csv26import re27from datetime import datetime2829INPUT_EX = "/app/input/ex.csv"30OUTPUT_ADEX = "/app/output/adex.csv"3132COLUMNS = [33    "STUDYID",34    "USUBJID",35    "EXSEQ",36    "EXSTDTC",37    "EXENDTC",38    "EXDUR",39    "PARAMCD",40    "PARAM",41    "AVAL",42    "CALCDUR",43]4445# A fixed-length ISO 8601 duration: P[nD][T[nH][nM][nS]] with at least46# one component. Years, months and weeks are not fixed length, so a47# duration using them is not readable here.48DURATION_RE = re.compile(49    r"^P(?:(?P<days>\d+(?:\.\d+)?)D)?"50    r"(?:T(?:(?P<hours>\d+(?:\.\d+)?)H)?"51    r"(?:(?P<minutes>\d+(?:\.\d+)?)M)?"52    r"(?:(?P<seconds>\d+(?:\.\d+)?)S)?)?$"53)545556def parse_duration_minutes(text):57    """Minutes in a fixed-length ISO 8601 duration, or None."""58    if not text:59        return None60    match = DURATION_RE.match(text.strip())61    if match is None:62        return None63    parts = match.groupdict()64    if all(value is None for value in parts.values()):65        return None66    total = 0.067    if parts["days"] is not None:68        total += float(parts["days"]) * 1440.069    if parts["hours"] is not None:70        total += float(parts["hours"]) * 60.071    if parts["minutes"] is not None:72        total += float(parts["minutes"])73    if parts["seconds"] is not None:74        total += float(parts["seconds"]) / 60.075    return total767778def parse_datetime(text):79    """A datetime for an ISO 8601 value that carries a time of day,80    or None when the value is a date without a time (or missing)."""81    if not text:82        return None83    text = text.strip()84    if "T" not in text:85        return None86    return datetime.fromisoformat(text)878889def calc_duration_minutes(start_text, end_text):90    """Elapsed minutes from start to end, or None when either value91    was collected as a date without a time of day."""92    start = parse_datetime(start_text)93    end = parse_datetime(end_text)94    if start is None or end is None:95        return None96    return (end - start).total_seconds() / 60.0979899def format_number(value):100    """A number as text: whole minutes without a decimal point,101    otherwise the exact value (no rounding beyond float repr)."""102    if value is None:103        return ""104    if float(value).is_integer():105        return str(int(value))106    return repr(float(value))107108109def main():110    with open(INPUT_EX, newline="", encoding="utf-8") as handle:111        ex_rows = list(csv.DictReader(handle))112113    out_rows = []114    for row in ex_rows:115        calcdur = calc_duration_minutes(row["EXSTDTC"], row["EXENDTC"])116        collected = parse_duration_minutes(row["EXDUR"])117        aval = collected if collected is not None else calcdur118        out_rows.append(119            {120                "STUDYID": row["STUDYID"],121                "USUBJID": row["USUBJID"],122                "EXSEQ": row["EXSEQ"],123                "EXSTDTC": row["EXSTDTC"],124                "EXENDTC": row["EXENDTC"],125                "EXDUR": row["EXDUR"],126                "PARAMCD": "INFDUR",127                "PARAM": "Infusion Duration (min)",128                "AVAL": format_number(aval),129                "CALCDUR": format_number(calcdur),130            }131        )132133    with open(OUTPUT_ADEX, "w", newline="", encoding="utf-8") as handle:134        writer = csv.DictWriter(handle, fieldnames=COLUMNS)135        writer.writeheader()136        writer.writerows(out_rows)137138139if __name__ == "__main__":140    main()

1/* opensas reference solution for the yamaa benchmark adam-adex-infusion-duration.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data ex;6  length STUDYID USUBJID EXTRT EXROUTE EXSTDTC EXENDTC EXDUR $1024;7  infile "/app/input/ex.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. EXSEQ EXTRT : $char1024. EXROUTE : $char1024.9        EXSTDTC : $char1024. EXENDTC : $char1024. EXDUR : $char1024.;10run;1112/* A date alone has no time of day, and none is assumed; a time without13   seconds counts as second zero. An ISO 8601 duration of days, hours,14   minutes and seconds wins; anything else counts as not collected. */15data final;16  length PARAMCD $6 PARAM $23;17  set ex;18  PARAMCD='INFDUR'; PARAM='Infusion Duration (min)';19  st=.; en=.;20  if lengthn(EXSTDTC)>10 then st=input(cats(EXSTDTC, ifc(lengthn(EXSTDTC)=16, ':00', '')), e8601dt.);21  if lengthn(EXENDTC)>10 then en=input(cats(EXENDTC, ifc(lengthn(EXENDTC)=16, ':00', '')), e8601dt.);22  CALCDUR=.;23  if not missing(st) and not missing(en) then CALCDUR=(en-st)/60;24  COLL=.;25  rx=prxparse('/^P(?:(\d+)D)?(?:T(?:(\d+)H)?(?:(\d+)M)?(?:(\d+(?:\.\d+)?)S)?)?$/');26  if not missing(EXDUR) and prxmatch(rx, strip(EXDUR)) and lengthn(EXDUR)>1 and substr(EXDUR, lengthn(EXDUR), 1) ne 'T' then do;27    d=input(prxposn(rx, 1, strip(EXDUR)), ?? best.);28    h=input(prxposn(rx, 2, strip(EXDUR)), ?? best.);29    m=input(prxposn(rx, 3, strip(EXDUR)), ?? best.);30    s=input(prxposn(rx, 4, strip(EXDUR)), ?? best.);31    COLL=sum(0, d*1440, h*60, m, s/60);32  end;33  AVAL=coalesce(COLL, CALCDUR);34  format AVAL CALCDUR best32.;35  keep STUDYID USUBJID EXSEQ EXSTDTC EXENDTC EXDUR PARAMCD PARAM AVAL CALCDUR;36run;3738proc sql;39  create table out as select STUDYID, USUBJID, EXSEQ, EXSTDTC, EXENDTC, EXDUR, PARAMCD, PARAM, AVAL, CALCDUR40    from final;41quit;42proc export data=out outfile="/app/output/adex.csv" dbms=csv replace; run;