Combination Regimen

1library(yamaa)23ex <- yamaa_domain("spec.yaml")$output4ex

1import yamaa23ex = yamaa.yamaa_domain("spec.yaml").output4ex

1# Reference solution for the yamaa benchmark sdtm-ex-combination (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)910ex_raw <- read_csv(11  "/app/input/ex_raw.csv",12  col_types = cols(.default = col_character())13)1415ex <- ex_raw |>16  mutate(17    DOMAIN = "EX",18    EXDOSE = suppressWarnings(as.numeric(EXDOSE)),19    EXSTDTC_DATE = suppressWarnings(as.Date(EXSTDTC)),20    EXADJ = na_if(EXADJ, "")21  ) |>22  arrange(STUDYID, USUBJID, EXSTDTC_DATE, EXTRT) |>23  group_by(STUDYID, USUBJID) |>24  mutate(EXSEQ = row_number()) |>25  ungroup() |>26  select(27    DOMAIN, STUDYID, USUBJID, EXSEQ, EXTRT, EXDOSE, EXDOSU,28    EXSTDTC, EXENDTC, EXADJ29  )3031dir.create("/app/output", showWarnings = FALSE)32write_csv(ex, "/app/output/ex.csv", na = "")

1# Reference solution for the yamaa benchmark sdtm-ex-combination (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 pl1011ex_raw = pl.read_csv("/app/input/ex_raw.csv", infer_schema=False)1213ex = (14    ex_raw.with_columns(15        DOMAIN=pl.lit("EX"),16        EXDOSE=pl.col("EXDOSE").cast(pl.Float64, strict=False),17        EXSTDTC_DT=pl.col("EXSTDTC").str.to_date(strict=False),18        EXADJ=pl.col("EXADJ").map_elements(19            lambda v: None if v == "" or v is None else v, return_dtype=pl.String20        ),21    )22    .sort(["STUDYID", "USUBJID", "EXSTDTC_DT", "EXTRT"])23    .with_columns(EXSEQ=pl.col("USUBJID").cum_count().over(["STUDYID", "USUBJID"]))24    .with_columns(EXSEQ=pl.col("EXSEQ").cast(pl.Int64))25    .select(26        "DOMAIN",27        "STUDYID",28        "USUBJID",29        "EXSEQ",30        "EXTRT",31        "EXDOSE",32        "EXDOSU",33        "EXSTDTC",34        "EXENDTC",35        "EXADJ",36    )37)3839Path("/app/output").mkdir(exist_ok=True)40ex.write_csv("/app/output/ex.csv")

1/* opensas reference solution for the yamaa benchmark sdtm-ex-combination.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data ex_raw;6  length STUDYID USUBJID EXTRT EXDOSU EXSTDTC EXENDTC EXADJ $1024;7  infile "/app/input/ex_raw.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. EXTRT : $char1024. EXDOSE EXDOSU : $char1024. EXSTDTC : $char1024. EXENDTC : $char1024. EXADJ : $char1024.;9run;1011data prepared; set ex_raw; length DOMAIN $2; DOMAIN='EX'; run;12proc sort data=prepared; by STUDYID USUBJID EXSTDTC EXTRT; run;13data result; set prepared; by STUDYID USUBJID; retain EXSEQ;14  if first.USUBJID then EXSEQ=0;15  EXSEQ+1;16run;1718proc sql;19  create table final as select DOMAIN, STUDYID, USUBJID, EXSEQ, EXTRT, EXDOSE, EXDOSU, EXSTDTC, EXENDTC, EXADJ from result;20quit;21proc export data=final outfile="/app/output/ex.csv" dbms=csv replace; run;