Name Each Event's Prior Serious Event

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-prior-serious-event (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)1415serious <- ae |>16  filter(AESER %in% "Y") |>17  arrange(USUBJID, AESEQ)1819# The subject's first serious event, whatever its term holds.20first_sae <- serious |>21  distinct(USUBJID, .keep_all = TRUE) |>22  select(USUBJID, FIRST_SAEDECOD = AEDECOD, FIRST_SAESEQ = AESEQ)2324adae <- ae |>25  left_join(first_sae, by = "USUBJID") |>26  group_by(USUBJID) |>27  arrange(AESEQ, .by_group = TRUE) |>28  mutate(29    # The most recent earlier serious event, by sequence number.30    PRIOR_SAESEQ = sapply(31      AESEQ,32      function(s) {33        earlier <- AESEQ[AESER %in% "Y" & AESEQ < s]34        if (length(earlier) == 0L) NA_integer_ else max(earlier)35      }36    ),37    PRIOR_SAEDECOD = sapply(38      PRIOR_SAESEQ,39      function(s) {40        if (is.na(s)) NA_character_ else AEDECOD[match(s, AESEQ)]41      }42    ),43    PREV_SEQ = sapply(44      AESEQ,45      function(s) {46        earlier <- AESEQ[AESEQ < s]47        if (length(earlier) == 0L) NA_integer_ else max(earlier)48      }49    ),50    PREV_AEDECOD = sapply(51      PREV_SEQ,52      function(s) {53        if (is.na(s)) NA_character_ else AEDECOD[match(s, AESEQ)]54      }55    ),56    PREV_AEDECOD = if_else(57      PREV_AEDECOD == "" | is.na(PREV_AEDECOD),58      NA_character_,59      PREV_AEDECOD60    ),61    PRIOR_SAEDECOD = if_else(62      PRIOR_SAEDECOD == "" | is.na(PRIOR_SAEDECOD),63      NA_character_,64      PRIOR_SAEDECOD65    ),66    FIRST_SAEDECOD = if_else(67      FIRST_SAEDECOD == "" | is.na(FIRST_SAEDECOD),68      NA_character_,69      FIRST_SAEDECOD70    )71  ) |>72  ungroup() |>73  mutate(74    # A serious event leaves its own prior and first fields empty.75    PRIOR_SAEFL = if_else(76      AESER %in% "N" & !is.na(PRIOR_SAESEQ),77      "Y",78      NA_character_79    ),80    PRIOR_SAEDECOD = if_else(AESER %in% "N", PRIOR_SAEDECOD, NA_character_),81    PRIOR_SAESEQ = if_else(AESER %in% "N", PRIOR_SAESEQ, NA_integer_),82    FIRST_SAEDECOD = if_else(AESER %in% "N", FIRST_SAEDECOD, NA_character_),83    FIRST_SAESEQ = if_else(AESER %in% "N", FIRST_SAESEQ, NA_integer_)84  ) |>85  select(86    STUDYID, USUBJID, AESEQ, AEDECOD, AESER, PRIOR_SAEFL, PRIOR_SAEDECOD,87    PRIOR_SAESEQ, FIRST_SAEDECOD, FIRST_SAESEQ, PREV_AEDECOD88  )8990dir.create("/app/output", showWarnings = FALSE)91write_csv(adae, "/app/output/adae.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adae-prior-serious-event (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)1415records = []16for subject, group in ae.sort(["USUBJID", "AESEQ"]).group_by("USUBJID", maintain_order=True):17    rows = group.sort("AESEQ").to_dicts()18    serious_seqs = [r["AESEQ"] for r in rows if r["AESER"] == "Y"]19    first_seq = min(serious_seqs) if serious_seqs else None20    first_term = next(21        (r["AEDECOD"] for r in rows if r["AESEQ"] == first_seq), None22    )23    by_seq = {r["AESEQ"]: r for r in rows}24    for row in rows:25        seq = row["AESEQ"]26        earlier_serious = [s for s in serious_seqs if s < seq]27        prior_seq = max(earlier_serious) if earlier_serious else None28        prior_term = by_seq.get(prior_seq, {}).get("AEDECOD") if prior_seq else None29        earlier_all = [r["AESEQ"] for r in rows if r["AESEQ"] < seq]30        prev_seq = max(earlier_all) if earlier_all else None31        prev_term = by_seq.get(prev_seq, {}).get("AEDECOD") if prev_seq else None32        is_nonserious = row["AESER"] == "N"33        # Only an explicit N receives prior and first serious-event fields. A34        # serious event with no coded term still counts for the flag and35        # the sequence number, while the term fields stay empty.36        records.append(37            {38                "STUDYID": row["STUDYID"],39                "USUBJID": row["USUBJID"],40                "AESEQ": seq,41                "AEDECOD": row["AEDECOD"],42                "AESER": row["AESER"],43                "PRIOR_SAEFL": None44                if not is_nonserious or prior_seq is None45                else "Y",46                "PRIOR_SAEDECOD": None if not is_nonserious else prior_term,47                "PRIOR_SAESEQ": None if not is_nonserious else prior_seq,48                "FIRST_SAEDECOD": None if not is_nonserious else first_term,49                "FIRST_SAESEQ": None if not is_nonserious else first_seq,50                "PREV_AEDECOD": prev_term,51            }52        )5354adae = pl.DataFrame(55    records,56    schema={57        "STUDYID": pl.String,58        "USUBJID": pl.String,59        "AESEQ": pl.Int64,60        "AEDECOD": pl.String,61        "AESER": pl.String,62        "PRIOR_SAEFL": pl.String,63        "PRIOR_SAEDECOD": pl.String,64        "PRIOR_SAESEQ": pl.Int64,65        "FIRST_SAEDECOD": pl.String,66        "FIRST_SAESEQ": pl.Int64,67        "PREV_AEDECOD": pl.String,68    },69)7071Path("/app/output").mkdir(exist_ok=True)72adae.write_csv("/app/output/adae.csv")

1/* opensas reference solution for the yamaa benchmark adam-adae-prior-serious-event.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 AEDECOD AESER $1024;7  infile "/app/input/ae.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. AESEQ AEDECOD : $char1024. AESER : $char1024.;9run;1011proc sort data=ae(where=(AESER='Y')) out=serious; by STUDYID USUBJID AESEQ; run;12data firsts; set serious; by STUDYID USUBJID; if first.USUBJID; run;13proc sql; create table joined as select a.*,b.AEDECOD as firstterm,b.AESEQ as firstseq from ae as a left join firsts as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID; quit;14proc sort data=joined; by STUDYID USUBJID AESEQ; run;15data result;16  length PRIOR_SAEFL $1 PRIOR_SAEDECOD FIRST_SAEDECOD PREV_AEDECOD lastterm prevterm $1024;17  retain lastterm lastseq prevterm;18  set joined; by STUDYID USUBJID;19  if first.USUBJID then do; lastterm=''; lastseq=.; prevterm=''; end;20  PREV_AEDECOD=prevterm;21  if AESER='N' then do;22    PRIOR_SAEDECOD=lastterm; PRIOR_SAESEQ=lastseq;23    FIRST_SAEDECOD=firstterm; FIRST_SAESEQ=firstseq;24    if not missing(lastseq) then PRIOR_SAEFL='Y';25  end;26  if AESER='Y' then do; lastterm=AEDECOD; lastseq=AESEQ; end;27  prevterm=AEDECOD;28run;2930proc sql;31  create table final as select STUDYID, USUBJID, AESEQ, AEDECOD, AESER, PRIOR_SAEFL, PRIOR_SAEDECOD, PRIOR_SAESEQ, FIRST_SAEDECOD, FIRST_SAESEQ, PREV_AEDECOD from result;32quit;33proc export data=final outfile="/app/output/adae.csv" dbms=csv replace; run;