Partial Date 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-dates (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)1112ae <- read_csv(13  "/app/input/ae.csv",14  col_types = cols(AESEQ = col_integer(), .default = col_character())15)16adsl <- read_csv(17  "/app/input/adsl.csv",18  col_types = cols(TRTSDT = col_date(), .default = col_character())19) |>20  select(USUBJID, TRTSDT)2122adae <- ae |>23  left_join(adsl, by = "USUBJID") |>24  mutate(25    is_full = str_detect(AESTDTC, "^\\d{4}-\\d{2}-\\d{2}$"),26    is_month = str_detect(AESTDTC, "^\\d{4}-\\d{2}$"),27    # A year and month is completed to the 15th.28    completed = if_else(29      is_month,30      ymd(paste0(AESTDTC, "-15"), quiet = TRUE),31      ymd(AESTDTC, quiet = TRUE)32    ),33    completed = if_else(is_full | is_month, completed, as.Date(NA)),34    # A supplied day is never placed before a first exposure that falls35    # inside the collected month. When the whole collected month ends36    # before the exposure date, no day it allows could reach it, so the37    # date stays on the 15th.38    month_end = if_else(39      is_month,40      completed + days(days_in_month(completed) - 15L),41      completed42    ),43    month_before_trt = is_month &44      !is.na(month_end) & !is.na(TRTSDT) & month_end < TRTSDT,45    ASTDT = case_when(46      month_before_trt ~ completed,47      is_month & !is.na(completed) & !is.na(TRTSDT) & completed < TRTSDT ~ TRTSDT,48      .default = completed49    ),50    ASTDTC = if_else(is.na(ASTDT), NA_character_, as.character(ASTDT)),51    ASTDTF = if_else(is_month & !is.na(ASTDT), "D", NA_character_),52    TRTEMFL = if_else(53      !is.na(ASTDT) & !is.na(TRTSDT) & ASTDT >= TRTSDT,54      "Y",55      NA_character_56    )57  ) |>58  select(59    STUDYID, USUBJID, AESEQ, AETERM, AESTDTC, ASTDT, ASTDTC, ASTDTF,60    TRTSDT, TRTEMFL61  )6263dir.create("/app/output", showWarnings = FALSE)64write_csv(adae, "/app/output/adae.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adae-partial-dates (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 ADAE from ADSL and AE, completing partial AE start dates.89ASTDT is the adverse event start date derived from the collected10AESTDTC character date:1112- a full date is kept exactly as collected, even before treatment start;13- a year and month only is completed to the 15th of that month, except14  that when the 15th falls before TRTSDT within the same month ASTDT is15  TRTSDT; when the whole month falls before TRTSDT the 15th stands;16- a year only, non-date text, or a missing value gives no ASTDT.1718ASTDTF is "D" when a day was supplied to complete a year and month.19TRTEMFL is "Y" when ASTDT falls on or after TRTSDT.20"""2122import csv23import os24import re25from datetime import date2627INPUT_DIR = "/app/input"28OUTPUT_DIR = "/app/output"2930FULL_DATE = re.compile(r"^(\d{4})-(\d{2})-(\d{2})$")31YEAR_MONTH = re.compile(r"^(\d{4})-(\d{2})$")323334def parse_full_date(text):35    """Return a date for a strict YYYY-MM-DD string, else None."""36    match = FULL_DATE.match(text or "")37    if not match:38        return None39    try:40        return date(int(match.group(1)), int(match.group(2)), int(match.group(3)))41    except ValueError:42        return None434445def derive_astdt(aestdtc, trtsdt):46    """Return (ASTDT as a date or None, day-imputed flag)."""47    aestdtc = (aestdtc or "").strip()48    full = parse_full_date(aestdtc)49    if full is not None:50        return full, False51    match = YEAR_MONTH.match(aestdtc)52    if match:53        year, month = int(match.group(1)), int(match.group(2))54        if not 1 <= month <= 12:55            return None, False56        candidate = date(year, month, 15)57        if trtsdt is None or candidate >= trtsdt:58            return candidate, True59        if trtsdt.year == year and trtsdt.month == month:60            return trtsdt, True61        # The whole month falls before TRTSDT, so the 15th stands.62        return candidate, True63    return None, False646566def main():67    with open(os.path.join(INPUT_DIR, "adsl.csv"), newline="") as handle:68        adsl = list(csv.DictReader(handle))69    with open(os.path.join(INPUT_DIR, "ae.csv"), newline="") as handle:70        ae = list(csv.DictReader(handle))7172    trtsdt_by_subject = {}73    for row in adsl:74        trtsdt_by_subject[row["USUBJID"]] = parse_full_date(row.get("TRTSDT"))7576    columns = [77        "STUDYID", "USUBJID", "AESEQ", "AETERM", "AESTDTC",78        "ASTDT", "ASTDTC", "ASTDTF", "TRTSDT", "TRTEMFL",79    ]80    out_rows = []81    for row in ae:82        trtsdt = trtsdt_by_subject.get(row["USUBJID"])83        astdt, day_imputed = derive_astdt(row.get("AESTDTC"), trtsdt)84        astdtc = astdt.isoformat() if astdt is not None else ""85        astdtf = "D" if (day_imputed and astdt is not None) else ""86        trtemfl = ""87        if astdt is not None and trtsdt is not None and astdt >= trtsdt:88            trtemfl = "Y"89        out_rows.append({90            "STUDYID": row["STUDYID"],91            "USUBJID": row["USUBJID"],92            "AESEQ": row["AESEQ"],93            "AETERM": row["AETERM"],94            "AESTDTC": row["AESTDTC"],95            "ASTDT": astdt.isoformat() if astdt is not None else "",96            "ASTDTC": astdtc,97            "ASTDTF": astdtf,98            "TRTSDT": trtsdt.isoformat() if trtsdt is not None else "",99            "TRTEMFL": trtemfl,100        })101102    os.makedirs(OUTPUT_DIR, exist_ok=True)103    with open(os.path.join(OUTPUT_DIR, "adae.csv"), "w", newline="") as handle:104        writer = csv.DictWriter(handle, fieldnames=columns)105        writer.writeheader()106        writer.writerows(out_rows)107108109if __name__ == "__main__":110    main()

1/* opensas reference solution for the yamaa benchmark adam-adae-partial-dates.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 TRTSDT $1024;7  infile "/app/input/adsl.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. TRTSDT : $char1024.;9run;1011data ae;12  length STUDYID USUBJID AETERM AESTDTC $1024;13  infile "/app/input/ae.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024. AESEQ AETERM : $char1024. AESTDTC : $char1024.;15run;1617proc sql; create table joined as select a.*,b.TRTSDT from ae as a left join adsl as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID; quit;18data result;19  length ASTDT ASTDTC $10 ASTDTF TRTEMFL $1;20  set joined;21  treatment=input(TRTSDT,yymmdd10.); analysis=.;22  if prxmatch('/^[0-9]{4}-[0-9]{2}-[0-9]{2}$/',strip(AESTDTC)) then analysis=input(AESTDTC,yymmdd10.);23  else if prxmatch('/^[0-9]{4}-[0-9]{2}$/',strip(AESTDTC)) then do;24    analysis=input(cats(AESTDTC,'-15'),yymmdd10.);25    if not missing(analysis) then do;26      /* First exposure moves the 15th forward only when it falls inside the27         collected month; when it falls after the whole month, the 15th stands. */28      if missing(treatment) or treatment<=intnx('month',analysis,0,'end') then analysis=max(analysis,treatment);29      ASTDTF='D';30    end;31  end;32  if not missing(analysis) then do;33    ASTDT=put(analysis,yymmdd10.); ASTDTC=ASTDT;34    if not missing(treatment) and analysis>=treatment then TRTEMFL='Y';35  end;36run;3738proc sql;39  create table final as select STUDYID, USUBJID, AESEQ, AETERM, AESTDTC, ASTDT, ASTDTC, ASTDTF, TRTSDT, TRTEMFL from result;40quit;41proc export data=final outfile="/app/output/adae.csv" dbms=csv replace; run;