Partial Time Imputation

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

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

1# Reference solution for the yamaa benchmark adam-adae-partial-times (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)910ae <- read_csv(11  "/app/input/ae.csv",12  col_types = cols(AESEQ = col_integer(), .default = col_character())13)1415# Complete a collected value by its length: the missing parts take their16# earliest (start) or latest (end) values. A value without its day, or no17# value at all, gives no analysis time.18complete_time <- function(x, last) {19  n <- nchar(x)20  case_when(21    n == 19 ~ x,22    n == 16 ~ paste0(x, if (last) ":59" else ":00"),23    n == 13 ~ paste0(x, if (last) ":59:59" else ":00:00"),24    n == 10 ~ paste0(x, if (last) "T23:59:59" else "T00:00:00"),25    TRUE ~ NA_character_26  )27}2829# The flag names the coarsest part of the time that was supplied.30time_flag <- function(x) {31  n <- nchar(x)32  case_when(33    n == 16 ~ "S",34    n == 13 ~ "M",35    n == 10 ~ "H",36    TRUE ~ NA_character_37  )38}3940adae <- ae |>41  mutate(42    ASTDTM = complete_time(AESTDTC, last = FALSE),43    ASTTMF = time_flag(AESTDTC),44    AENDTM = complete_time(AEENDTC, last = TRUE),45    AENTMF = time_flag(AEENDTC)46  ) |>47  select(48    STUDYID, USUBJID, AESEQ, AETERM, AESTDTC, ASTDTM, ASTTMF,49    AEENDTC, AENDTM, AENTMF50  )5152dir.create("/app/output", showWarnings = FALSE)53write_csv(adae, "/app/output/adae.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adae-partial-times (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 ADAE from AE, completing partial start/end datetimes.89ASTDTM completes AESTDTC with the earliest value of each uncollected10time part; AENDTM completes AEENDTC with the latest value. The time11imputation flags record what was collected: "H" for a date alone,12"M" for collection to the hour, "S" for collection to the minute,13and no value when collected to the second or when no datetime can14be formed (day not collected).15"""1617import csv18import re1920INPUT_PATH = "/app/input/ae.csv"21OUTPUT_PATH = "/app/output/adae.csv"2223SECOND = re.compile(r"^\d{4}-\d{2}-\d{2}T\d{2}:\d{2}:\d{2}$")24MINUTE = re.compile(r"^\d{4}-\d{2}-\d{2}T\d{2}:\d{2}$")25HOUR = re.compile(r"^\d{4}-\d{2}-\d{2}T\d{2}$")26DATE = re.compile(r"^\d{4}-\d{2}-\d{2}$")272829def complete(value, end):30    """Return (datetime_text, flag) completing a partial ISO datetime.3132    `end` selects latest-value completion instead of earliest-value.33    """34    value = (value or "").strip()35    if not value:36        return "", ""37    if SECOND.match(value):38        return value, ""39    if MINUTE.match(value):40        seconds = "59" if end else "00"41        return value + ":" + seconds, "S"42    if HOUR.match(value):43        tail = ":59:59" if end else ":00:00"44        return value + tail, "M"45    if DATE.match(value):46        tail = "T23:59:59" if end else "T00:00:00"47        return value + tail, "H"48    # Collected without its day (e.g. year-month only): no datetime.49    return "", ""505152def main():53    with open(INPUT_PATH, newline="", encoding="utf-8") as f:54        rows = list(csv.DictReader(f))5556    out_rows = []57    for row in rows:58        astdtm, asttmf = complete(row["AESTDTC"], end=False)59        aendtm, aentmf = complete(row["AEENDTC"], end=True)60        out_rows.append(61            {62                "STUDYID": row["STUDYID"],63                "USUBJID": row["USUBJID"],64                "AESEQ": row["AESEQ"],65                "AETERM": row["AETERM"],66                "AESTDTC": row["AESTDTC"],67                "ASTDTM": astdtm,68                "ASTTMF": asttmf,69                "AEENDTC": row["AEENDTC"],70                "AENDTM": aendtm,71                "AENTMF": aentmf,72            }73        )7475    fieldnames = [76        "STUDYID",77        "USUBJID",78        "AESEQ",79        "AETERM",80        "AESTDTC",81        "ASTDTM",82        "ASTTMF",83        "AEENDTC",84        "AENDTM",85        "AENTMF",86    ]87    with open(OUTPUT_PATH, "w", newline="", encoding="utf-8") as f:88        writer = csv.DictWriter(f, fieldnames=fieldnames)89        writer.writeheader()90        writer.writerows(out_rows)919293if __name__ == "__main__":94    main()

1/* opensas reference solution for the yamaa benchmark adam-adae-partial-times.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data ae;6  length STUDYID USUBJID AETERM AESTDTC AEENDTC $1024;7  infile "/app/input/ae.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. AESEQ AETERM : $char1024. AESTDTC : $char1024. AEENDTC : $char1024.;9run;1011/* Complete each collected value by its length: the missing parts take their12   earliest (start) or latest (end) values, and the flag names the coarsest13   part supplied. A value without its day, or no value, gives no time. */14data result;15  length ASTDTM AENDTM $19 ASTTMF AENTMF $1;16  set ae;17  ASTDTM=''; ASTTMF=''; AENDTM=''; AENTMF='';18  ls=lengthn(AESTDTC);19  if ls=19 then ASTDTM=AESTDTC;20  else if ls=16 then do; ASTDTM=cats(AESTDTC, ':00'); ASTTMF='S'; end;21  else if ls=13 then do; ASTDTM=cats(AESTDTC, ':00:00'); ASTTMF='M'; end;22  else if ls=10 then do; ASTDTM=cats(AESTDTC, 'T00:00:00'); ASTTMF='H'; end;23  le=lengthn(AEENDTC);24  if le=19 then AENDTM=AEENDTC;25  else if le=16 then do; AENDTM=cats(AEENDTC, ':59'); AENTMF='S'; end;26  else if le=13 then do; AENDTM=cats(AEENDTC, ':59:59'); AENTMF='M'; end;27  else if le=10 then do; AENDTM=cats(AEENDTC, 'T23:59:59'); AENTMF='H'; end;28run;2930proc sql;31  create table final as select STUDYID, USUBJID, AESEQ, AETERM, AESTDTC, ASTDTM, ASTTMF,32    AEENDTC, AENDTM, AENTMF from result;33quit;34proc export data=final outfile="/app/output/adae.csv" dbms=csv replace; run;