Serious Event Sequence

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-serious-sequence (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)910ae <- read_csv(11  "/app/input/ae.csv",12  col_types = cols(AESEQ = col_integer(), .default = col_character())13)1415# Number the subject's serious events in onset order, so the earliest16# carries 1. Events sharing one onset date follow collection order, and17# a serious event with no onset date is numbered last.18numbered <- ae |>19  filter(AESER %in% "Y") |>20  mutate(ASTDT = if_else(is.na(AESTDTC) | AESTDTC == "", NA_character_, AESTDTC)) |>21  arrange(USUBJID, is.na(ASTDT), ASTDT, AESEQ) |>22  group_by(USUBJID) |>23  mutate(SERSEQ = row_number()) |>24  ungroup() |>25  select(USUBJID, AESEQ, SERSEQ)2627adae <- ae |>28  mutate(ASTDT = if_else(is.na(AESTDTC) | AESTDTC == "", NA_character_, AESTDTC)) |>29  left_join(numbered, by = c("USUBJID", "AESEQ")) |>30  select(STUDYID, USUBJID, AESEQ, AESER, ASTDT, SERSEQ)3132dir.create("/app/output", showWarnings = FALSE)33write_csv(adae, "/app/output/adae.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adae-serious-sequence (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 pl1011ae = pl.read_csv("/app/input/ae.csv", infer_schema=False).with_columns(12    pl.col("AESEQ").cast(pl.Int64)13)1415# Number the subject's serious events in onset order, so the earliest16# carries 1. Events sharing one onset date follow collection order, and17# a serious event with no onset date is numbered last. ISO dates sort18# as text. Numbering restarts for each subject.19numbered = (20    ae.filter(pl.col("AESER") == "Y")21    .with_columns(ASTDT=pl.col("AESTDTC"))22    .sort(["USUBJID", "AESTDTC", "AESEQ"], nulls_last=True)23    .with_columns(SERSEQ=pl.col("AESEQ").cum_count().over("USUBJID"))24    .select("USUBJID", "AESEQ", "SERSEQ")25)2627adae = (28    ae.with_columns(ASTDT=pl.col("AESTDTC"))29    .join(numbered, on=["USUBJID", "AESEQ"], how="left", maintain_order="left")30    .select("STUDYID", "USUBJID", "AESEQ", "AESER", "ASTDT", "SERSEQ")31)3233Path("/app/output").mkdir(exist_ok=True)34adae.write_csv("/app/output/adae.csv")

1/* opensas reference solution for the yamaa benchmark adam-adae-serious-sequence.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data ae;6  length STUDYID USUBJID AETERM AESER AESTDTC $1024;7  infile "/app/input/ae.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. AESEQ AETERM : $char1024. AESER : $char1024. AESTDTC : $char1024.;9run;1011data ordered; set ae; nodate=missing(AESTDTC); run;12proc sort data=ordered; by STUDYID USUBJID nodate AESTDTC AESEQ; run;13data result;14  length ASTDT $10;15  set ordered; by STUDYID USUBJID;16  if first.USUBJID then counter=0;17  ASTDT=AESTDTC;18  if AESER='Y' then do; counter+1; SERSEQ=counter; end;19run;2021proc sql;22  create table final as select STUDYID, USUBJID, AESEQ, AESER, ASTDT, SERSEQ from result;23quit;24proc export data=final outfile="/app/output/adae.csv" dbms=csv replace; run;