Select the Best Overall Response

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

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

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 1.67import csv89AVAL_BY_AVALC = {10    "CR": "1",11    "PR": "2",12    "SD": "3",13    "NON-CR/NON-PD": "4",14    "PD": "5",15    "NE": "6",16}1718with open("/app/input/adsl.csv", newline="") as f:19    adsl = list(csv.DictReader(f))2021with open("/app/input/adrs_selection.csv", newline="") as f:22    selection = list(csv.DictReader(f))2324best = {}25for row in selection:26    if row["BORSEQ"] == "1":27        best[row["USUBJID"]] = row2829out = []30for subj in adsl:31    usubjid = subj["USUBJID"]32    sel = best.get(usubjid)33    avalc = sel["BORCAT"] if sel else ""34    aval = AVAL_BY_AVALC[avalc] if avalc else ""35    adt = sel["ADT"] if sel else ""36    out.append(37        {38            "STUDYID": subj["STUDYID"],39            "USUBJID": usubjid,40            "PARAMCD": "BOR",41            "PARAM": "Best Overall Response by Investigator",42            "RANDDT": subj["RANDDT"],43            "AVALC": avalc,44            "AVAL": aval,45            "ADT": adt,46        }47    )4849fields = ["STUDYID", "USUBJID", "PARAMCD", "PARAM", "RANDDT", "AVALC", "AVAL", "ADT"]50with open("/app/output/adrs.csv", "w", newline="") as f:51    writer = csv.DictWriter(f, fieldnames=fields)52    writer.writeheader()53    writer.writerows(out)

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;