Prepare Response Assessments for 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-response-prep (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)910raw <- read_csv(11  "/app/input/adrs_raw.csv",12  col_types = cols(13    ASEQ = col_integer(),14    ADT = col_date(),15    RANDDY = col_integer(),16    .default = col_character()17  )18)1920therapy <- read_csv(21  "/app/input/adsl.csv",22  col_types = cols(23    NTXSTDT = col_date(),24    .default = col_character()25  )26)2728raw <- raw |>29  left_join(therapy, by = c("STUDYID", "USUBJID"))3031# The response category each record can support; an assessment on or after32# the subject's new anti-cancer therapy start supports no category. Stable33# and neither-complete-nor-progressive disease count only on or after day34# 42, and earlier ones, or ones with no day, fall back to not evaluable.35based <- raw |>36  mutate(37    BORCAT = case_when(38      !is.na(NTXSTDT) & ADT >= NTXSTDT ~ NA_character_,39      AVALC %in% c("CR", "PR", "PD", "NE") ~ AVALC,40      AVALC %in% "SD" & !is.na(RANDDY) & RANDDY >= 42L ~ "SD",41      AVALC %in% "SD" ~ "NE",42      AVALC %in% "NON-CR/NON-PD" & !is.na(RANDDY) & RANDDY >= 42L ~ "NON-CR/NON-PD",43      AVALC %in% "NON-CR/NON-PD" ~ "NE",44      .default = NA_character_45    ),46    BORPRI = case_when(47      BORCAT == "CR" ~ 1L,48      BORCAT == "PR" ~ 2L,49      BORCAT == "SD" ~ 3L,50      BORCAT == "NON-CR/NON-PD" ~ 4L,51      BORCAT == "PD" ~ 5L,52      BORCAT == "NE" ~ 6L53    )54  )5556# Usable records numbered from 1 in priority, date, then sequence order;57# records supporting no category are passed over without a gap.58order <- based |>59  filter(!is.na(BORCAT)) |>60  arrange(STUDYID, USUBJID, BORPRI, ADT, ASEQ) |>61  group_by(STUDYID, USUBJID) |>62  mutate(BORSEQ = row_number()) |>63  ungroup() |>64  select(STUDYID, USUBJID, ASEQ, BORSEQ)6566adrs <- based |>67  left_join(order, by = c("STUDYID", "USUBJID", "ASEQ")) |>68  select(STUDYID, USUBJID, ASEQ, ADT, RANDDY, AVALC, BORCAT, BORPRI, BORSEQ) |>69  arrange(STUDYID, USUBJID, ASEQ)7071dir.create("/app/output", showWarnings = FALSE)72write_csv(adrs, "/app/output/adrs.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adrs-response-prep (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 pl1011raw = pl.read_csv("/app/input/adrs_raw.csv", infer_schema=False).with_columns(12    pl.col("ASEQ").cast(pl.Int64),13    pl.col("ADT").str.to_date(),14    pl.col("RANDDY").cast(pl.Int64),15)1617therapy = pl.read_csv("/app/input/adsl.csv", infer_schema=False).with_columns(18    pl.col("NTXSTDT").str.to_date(),19)2021raw = raw.join(therapy, on=["STUDYID", "USUBJID"], how="left")2223# The response category each record can support; an assessment on or after24# the subject's new anti-cancer therapy start supports no category, and so25# do the usual suspects. Stable and neither-complete-nor-progressive26# disease count only on or after day 42, and earlier ones, or ones with no27# day, fall back to not evaluable.28based = raw.with_columns(29    BORCAT=pl.when(pl.col("NTXSTDT").is_not_null() & (pl.col("ADT") >= pl.col("NTXSTDT")))30    .then(pl.lit(None, dtype=pl.String))31    .when(pl.col("AVALC").is_in(["CR", "PR", "PD", "NE"]))32    .then(pl.col("AVALC"))33    .when((pl.col("AVALC") == "SD") & (pl.col("RANDDY") >= 42))34    .then(pl.lit("SD"))35    .when(pl.col("AVALC") == "SD")36    .then(pl.lit("NE"))37    .when((pl.col("AVALC") == "NON-CR/NON-PD") & (pl.col("RANDDY") >= 42))38    .then(pl.lit("NON-CR/NON-PD"))39    .when(pl.col("AVALC") == "NON-CR/NON-PD")40    .then(pl.lit("NE")),41).with_columns(42    BORPRI=pl.col("BORCAT").replace_strict(43        {"CR": 1, "PR": 2, "SD": 3, "NON-CR/NON-PD": 4, "PD": 5, "NE": 6},44        default=None,45        return_dtype=pl.Int64,46    )47)4849# Usable records numbered from 1 in priority, date, then sequence order;50# records supporting no category are passed over without a gap.51usable = (52    based.filter(pl.col("BORCAT").is_not_null())53    .sort(["STUDYID", "USUBJID", "BORPRI", "ADT", "ASEQ"])54    .with_columns(55        BORSEQ=pl.col("ASEQ").cum_count().over(["STUDYID", "USUBJID"]).cast(pl.Int64)56    )57    .select("STUDYID", "USUBJID", "ASEQ", "BORSEQ")58)5960adrs = (61    based.join(usable, on=["STUDYID", "USUBJID", "ASEQ"], how="left")62    .select(63        "STUDYID", "USUBJID", "ASEQ", "ADT", "RANDDY",64        "AVALC", "BORCAT", "BORPRI", "BORSEQ",65    )66    .sort(["STUDYID", "USUBJID", "ASEQ"])67)6869Path("/app/output").mkdir(exist_ok=True)70adrs.write_csv("/app/output/adrs.csv")

1/* opensas reference solution for the yamaa benchmark adam-adrs-response-prep.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data adrs_raw;6  length STUDYID USUBJID ADT RANDDY AVALC $1024;7  infile "/app/input/adrs_raw.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. ASEQ ADT : $char1024. RANDDY : $char1024. AVALC : $char1024.;9run;1011data adsl;12  length STUDYID USUBJID NTXSTDT $1024;13  infile "/app/input/adsl.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024. NTXSTDT : $char1024.;15run;1617proc sql; create table joined as select a.*,b.NTXSTDT from adrs_raw as a left join adsl as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID; quit;18data categories;19  length BORCAT $16;20  set joined;21  if AVALC in ('CR','PR','SD','NON-CR/NON-PD','PD','NE') and (missing(NTXSTDT) or ADT<NTXSTDT) then do;22    BORCAT=AVALC;23    if AVALC in ('SD','NON-CR/NON-PD') and (missing(RANDDY) or input(RANDDY,best32.)<42) then BORCAT='NE';24  end;25  select(BORCAT); when('CR') BORPRI=1; when('PR') BORPRI=2; when('SD') BORPRI=3; when('NON-CR/NON-PD') BORPRI=4; when('PD') BORPRI=5; when('NE') BORPRI=6; otherwise BORPRI=.; end;26  unusable=missing(BORPRI);27run;28proc sort data=categories; by STUDYID USUBJID unusable BORPRI ADT ASEQ; run;29data result;30  set categories; by STUDYID USUBJID;31  if first.USUBJID then sequence=0;32  if not missing(BORPRI) then do; sequence+1; BORSEQ=sequence; end;33run;3435proc sql;36  create table final as select STUDYID, USUBJID, ASEQ, ADT, RANDDY, AVALC, BORCAT, BORPRI, BORSEQ from result;37quit;38proc export data=final outfile="/app/output/adrs.csv" dbms=csv replace; run;