Partial Date Imputation

1library(yamaa)23adae <- yamaa_domain("spec.yaml")$output4adae

1import yamaa23adae = yamaa.yamaa_domain("spec.yaml").output4adae

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 completed date is never placed before first exposure. When the35    # whole collected month ends before the exposure date, no day it36    # allows can satisfy that, so the event is left without a date.37    month_end = if_else(38      is_month,39      completed + days(days_in_month(completed) - 15L),40      completed41    ),42    month_before_trt = is_month &43      !is.na(month_end) & !is.na(TRTSDT) & month_end < TRTSDT,44    ASTDT = case_when(45      month_before_trt ~ as.Date(NA),46      is_month & !is.na(completed) & !is.na(TRTSDT) & completed < TRTSDT ~ TRTSDT,47      .default = completed48    ),49    ASTDTC = if_else(is.na(ASTDT), NA_character_, as.character(ASTDT)),50    ASTDTF = if_else(is_month & !is.na(ASTDT), "D", NA_character_),51    TRTEMFL = if_else(52      !is.na(ASTDT) & !is.na(TRTSDT) & ASTDT >= TRTSDT,53      "Y",54      NA_character_55    )56  ) |>57  select(58    STUDYID, USUBJID, AESEQ, AETERM, AESTDTC, ASTDT, ASTDTC, ASTDTF,59    TRTSDT, TRTEMFL60  )6162dir.create("/app/output", showWarnings = FALSE)63write_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 1.67import calendar8from pathlib import Path910import polars as pl1112ae = pl.read_csv("/app/input/ae.csv", infer_schema=False).with_columns(13    pl.col("AESEQ").cast(pl.Int64)14)15adsl = pl.read_csv("/app/input/adsl.csv", infer_schema=False).select("USUBJID", "TRTSDT")161718def complete_row(collected: str | None, trt: str | None) -> tuple[str | None, str | None]:19    """The analysis date and its imputation flag for one collected start."""20    if collected is None:21        return None, None22    full = len(collected) == 10 and collected[4] == "-" and collected[7] == "-"23    month = len(collected) == 7 and collected[4] == "-"24    try:25        if full:26            year, mon, day = int(collected[0:4]), int(collected[5:7]), int(collected[8:10])27            last_day = calendar.monthrange(year, mon)[1]28            if day < 1 or day > last_day:29                return None, None30            completed = f"{year:04d}-{mon:02d}-{day:02d}"31            # A fully collected date stays exactly as collected.32            return completed, None33        if not month:34            return None, None35        year, mon = int(collected[0:4]), int(collected[5:7])36        completed = f"{year:04d}-{mon:02d}-15"37        if trt is None:38            return completed, "D"39        # A completed date is never placed before first exposure. When40        # the whole collected month ends before the exposure date, the41        # event is left without an analysis date.42        last_day = calendar.monthrange(year, mon)[1]43        month_end = f"{year:04d}-{mon:02d}-{last_day:02d}"44        if month_end < trt:45            return None, None46        if completed < trt:47            return trt, "D"48        return completed, "D"49    except ValueError:50        return None, None515253joined = ae.join(adsl, on="USUBJID", how="left", maintain_order="left")54records = []55for row in joined.to_dicts():56    ast, flag = complete_row(row["AESTDTC"], row["TRTSDT"])57    trtemfl = (58        "Y"59        if ast is not None and row["TRTSDT"] is not None and ast >= row["TRTSDT"]60        else None61    )62    records.append(63        {64            "STUDYID": row["STUDYID"],65            "USUBJID": row["USUBJID"],66            "AESEQ": row["AESEQ"],67            "AETERM": row["AETERM"],68            "AESTDTC": row["AESTDTC"],69            "ASTDT": ast,70            "ASTDTC": ast,71            "ASTDTF": flag,72            "TRTSDT": row["TRTSDT"],73            "TRTEMFL": trtemfl,74        }75    )7677adae = pl.DataFrame(78    records,79    schema={80        "STUDYID": pl.String,81        "USUBJID": pl.String,82        "AESEQ": pl.Int64,83        "AETERM": pl.String,84        "AESTDTC": pl.String,85        "ASTDT": pl.String,86        "ASTDTC": pl.String,87        "ASTDTF": pl.String,88        "TRTSDT": pl.String,89        "TRTEMFL": pl.String,90    },91)9293Path("/app/output").mkdir(exist_ok=True)94adae.write_csv("/app/output/adae.csv")

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      if not missing(treatment) and intnx('month',analysis,0,'end')<treatment then analysis=.;27      else do; analysis=max(analysis,treatment); ASTDTF='D'; end;28    end;29  end;30  if not missing(analysis) then do;31    ASTDT=put(analysis,yymmdd10.); ASTDTC=ASTDT;32    if not missing(treatment) and analysis>=treatment then TRTEMFL='Y';33  end;34run;3536proc sql;37  create table final as select STUDYID, USUBJID, AESEQ, AETERM, AESTDTC, ASTDT, ASTDTC, ASTDTF, TRTSDT, TRTEMFL from result;38quit;39proc export data=final outfile="/app/output/adae.csv" dbms=csv replace; run;