Select the Best Overall Response

1library(yamaa)23adrs <- yamaa_domain("spec.yaml")$output4adrs

1import yamaa23adrs = yamaa.yamaa_domain("spec.yaml").output4adrs

1# Reference solution for the yamaa benchmark adam-adrs-best-response (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)910adsl <- read_csv(11  "/app/input/adsl.csv",12  col_types = cols(RANDDT = col_date(), .default = col_character())13)14selection <- read_csv(15  "/app/input/adrs_selection.csv",16  col_types = cols(17    ASEQ = col_integer(),18    ADT = col_date(),19    RANDDY = col_integer(),20    BORPRI = col_integer(),21    BORSEQ = col_integer(),22    .default = col_character()23  )24)2526# The best overall response is the selection record numbered 1.27best <- selection |>28  filter(BORSEQ == 1L) |>29  select(USUBJID, BORCAT, BESTDT = ADT)3031adrs <- adsl |>32  left_join(best, by = "USUBJID") |>33  mutate(34    PARAMCD = "BOR",35    PARAM = "Best Overall Response by Investigator",36    AVALC = BORCAT,37    AVAL = case_when(38      AVALC == "CR" ~ 1L,39      AVALC == "PR" ~ 2L,40      AVALC == "SD" ~ 3L,41      AVALC == "NON-CR/NON-PD" ~ 4L,42      AVALC == "PD" ~ 5L,43      AVALC == "NE" ~ 6L44    ),45    ADT = BESTDT46  ) |>47  select(STUDYID, USUBJID, PARAMCD, PARAM, RANDDT, AVALC, AVAL, ADT) |>48  arrange(USUBJID)4950dir.create("/app/output", showWarnings = FALSE)51write_csv(adrs, "/app/output/adrs.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adrs-best-response (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 1.67from pathlib import Path89import polars as pl1011adsl = pl.read_csv("/app/input/adsl.csv", infer_schema=False).with_columns(12    pl.col("RANDDT").str.to_date()13)14selection = pl.read_csv(15    "/app/input/adrs_selection.csv", infer_schema=False16).with_columns(17    pl.col("ASEQ").cast(pl.Int64),18    pl.col("ADT").str.to_date(),19    pl.col("RANDDY").cast(pl.Int64),20    pl.col("BORPRI").cast(pl.Int64),21    pl.col("BORSEQ").cast(pl.Int64),22)2324# The best overall response is the selection record numbered 1.25best = selection.filter(pl.col("BORSEQ") == 1).select(26    "USUBJID", BORCAT="BORCAT", BESTDT="ADT"27)2829adrs = (30    adsl.join(best, on="USUBJID", how="left")31    .with_columns(32        PARAMCD=pl.lit("BOR"),33        PARAM=pl.lit("Best Overall Response by Investigator"),34        AVALC=pl.col("BORCAT"),35        AVAL=pl.col("BORCAT").replace_strict(36            {"CR": 1, "PR": 2, "SD": 3, "NON-CR/NON-PD": 4, "PD": 5, "NE": 6},37            default=None,38            return_dtype=pl.Int64,39        ),40        ADT=pl.col("BESTDT"),41    )42    .select("STUDYID", "USUBJID", "PARAMCD", "PARAM", "RANDDT", "AVALC", "AVAL", "ADT")43    .sort("USUBJID")44)4546Path("/app/output").mkdir(exist_ok=True)47adrs.write_csv("/app/output/adrs.csv")

1/* opensas reference solution for the yamaa benchmark adam-adrs-best-response.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data adrs_selection;6  length STUDYID USUBJID ADT RANDDY AVALC BORCAT BORPRI $1024;7  infile "/app/input/adrs_selection.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. ASEQ ADT : $char1024. RANDDY : $char1024. AVALC : $char1024. BORCAT : $char1024. BORPRI : $char1024. BORSEQ;9run;1011data adsl;12  length STUDYID USUBJID RANDDT $1024;13  infile "/app/input/adsl.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024. RANDDT : $char1024.;15run;1617proc sql; create table joined as select a.*,b.BORCAT as AVALC,b.ADT from adsl as a left join adrs_selection as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID and b.BORSEQ=1; quit;18data result;19  length PARAMCD $8 PARAM $40;20  set joined; PARAMCD='BOR'; PARAM='Best Overall Response by Investigator';21  select(AVALC); when('CR') AVAL=1; when('PR') AVAL=2; when('SD') AVAL=3; when('NON-CR/NON-PD') AVAL=4; when('PD') AVAL=5; when('NE') AVAL=6; otherwise AVAL=.; end;22  if missing(AVALC) then ADT='';23run;2425proc sql;26  create table final as select STUDYID, USUBJID, PARAMCD, PARAM, RANDDT, AVALC, AVAL, ADT from result;27quit;28proc export data=final outfile="/app/output/adrs.csv" dbms=csv replace; run;