Pair Each Adverse Event with Each Medication Related to It

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

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

1# Reference solution for the yamaa benchmark adam-adaecm-related-pairs (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 1.67read_text <- function(name) {8  read.csv(9    file.path("/app/input", name),10    colClasses = "character",11    na.strings = character(0),12    check.names = FALSE13  )14}1516ae <- read_text("ae.csv")17cm <- read_text("cm.csv")18relrec <- read_text("relrec.csv")1920events <- relrec[relrec$RDOMAIN == "AE" & relrec$IDVAR == "AESEQ",21                 c("STUDYID", "USUBJID", "RELID", "IDVARVAL")]22names(events)[4] <- "AESEQ"23medications <- relrec[relrec$RDOMAIN == "CM" & relrec$IDVAR == "CMSEQ",24                      c("STUDYID", "USUBJID", "RELID", "IDVARVAL")]25names(medications)[4] <- "CMSEQ"2627# Every event of a relationship with every medication of the same subject's28# same relationship.29pairs <- merge(events, medications, by = c("STUDYID", "USUBJID", "RELID"))30pairs$AESEQ <- as.integer(pairs$AESEQ)31pairs$CMSEQ <- as.integer(pairs$CMSEQ)3233pairs$AETERM <- ae$AETERM[match(34  paste(pairs$STUDYID, pairs$USUBJID, pairs$AESEQ, sep = "\r"),35  paste(ae$STUDYID, ae$USUBJID, as.integer(ae$AESEQ), sep = "\r")36)]37pairs$CMTRT <- cm$CMTRT[match(38  paste(pairs$STUDYID, pairs$USUBJID, pairs$CMSEQ, sep = "\r"),39  paste(cm$STUDYID, cm$USUBJID, as.integer(cm$CMSEQ), sep = "\r")40)]4142adaecm <- pairs[order(pairs$STUDYID, pairs$USUBJID, pairs$AESEQ, pairs$CMSEQ,43                      method = "radix"),44                c("STUDYID", "USUBJID", "AESEQ", "AETERM", "CMSEQ", "CMTRT",45                  "RELID")]4647dir.create("/app/output", showWarnings = FALSE, recursive = TRUE)48write.csv(adaecm, "/app/output/adaecm.csv", row.names = FALSE, na = "")

1# Reference solution for the yamaa benchmark adam-adaecm-related-pairs (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 csv8from pathlib import Path910INPUT_DIR = Path("/app/input")11OUTPUT_DIR = Path("/app/output")12COLUMNS = ["STUDYID", "USUBJID", "AESEQ", "AETERM", "CMSEQ", "CMTRT", "RELID"]131415def read(name: str) -> list[dict[str, str]]:16    with open(INPUT_DIR / name, newline="", encoding="utf-8") as handle:17        return list(csv.DictReader(handle))181920def main() -> None:21    ae = read("ae.csv")22    cm = read("cm.csv")23    relrec = read("relrec.csv")2425    terms = {(r["STUDYID"], r["USUBJID"], int(r["AESEQ"])): r["AETERM"] for r in ae}26    names = {(r["STUDYID"], r["USUBJID"], int(r["CMSEQ"])): r["CMTRT"] for r in cm}27    events = [r for r in relrec if r["RDOMAIN"] == "AE" and r["IDVAR"] == "AESEQ"]28    medications = [29        r for r in relrec if r["RDOMAIN"] == "CM" and r["IDVAR"] == "CMSEQ"30    ]3132    # Every event of a relationship with every medication of the same33    # subject's same relationship.34    rows = []35    for event in events:36        for medication in medications:37            if (event["STUDYID"], event["USUBJID"], event["RELID"]) != (38                medication["STUDYID"],39                medication["USUBJID"],40                medication["RELID"],41            ):42                continue43            aeseq = int(event["IDVARVAL"])44            cmseq = int(medication["IDVARVAL"])45            rows.append(46                {47                    "STUDYID": event["STUDYID"],48                    "USUBJID": event["USUBJID"],49                    "AESEQ": aeseq,50                    "AETERM": terms[(event["STUDYID"], event["USUBJID"], aeseq)],51                    "CMSEQ": cmseq,52                    "CMTRT": names[(event["STUDYID"], event["USUBJID"], cmseq)],53                    "RELID": event["RELID"],54                }55            )56    rows.sort(key=lambda r: (r["STUDYID"], r["USUBJID"], r["AESEQ"], r["CMSEQ"]))5758    OUTPUT_DIR.mkdir(parents=True, exist_ok=True)59    with open(OUTPUT_DIR / "adaecm.csv", "w", newline="", encoding="utf-8") as handle:60        writer = csv.writer(handle, lineterminator="\n")61        writer.writerow(COLUMNS)62        for row in rows:63            writer.writerow([row[column] for column in COLUMNS])646566if __name__ == "__main__":67    main()

1/* opensas reference solution for the yamaa benchmark adam-adaecm-related-pairs.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 DOMAIN USUBJID $40 AETERM $200;7  infile "/app/input/ae.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char40. DOMAIN : $char40. USUBJID : $char40. AESEQ9        AETERM : $char200.;10run;1112data cm;13  length STUDYID DOMAIN USUBJID $40 CMTRT $200;14  infile "/app/input/cm.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;15  input STUDYID : $char40. DOMAIN : $char40. USUBJID : $char40. CMSEQ16        CMTRT : $char200.;17run;1819data relrec;20  length STUDYID RDOMAIN USUBJID IDVAR IDVARVAL RELTYPE RELID $40;21  infile "/app/input/relrec.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;22  input STUDYID : $char40. RDOMAIN : $char40. USUBJID : $char40.23        IDVAR : $char40. IDVARVAL : $char40. RELTYPE : $char40.24        RELID : $char40.;25run;2627/* The events and the medications each relationship names, with their28   numeric sequence numbers. Function calls in join predicates were rejected29   by the release, and comparisons between identically named columns of a30   self-join gave incorrect results, so the two member lists are separate31   tables with their keys calculated before joining. */32data relae;33  set relrec;34  if RDOMAIN = 'AE' and IDVAR = 'AESEQ';35  AESEQ = input(IDVARVAL, best32.);36  keep STUDYID USUBJID RELID AESEQ;37run;3839data relcm;40  set relrec;41  if RDOMAIN = 'CM' and IDVAR = 'CMSEQ';42  CMSEQ = input(IDVARVAL, best32.);43  keep STUDYID USUBJID RELID CMSEQ;44run;4546proc sql;47  /* Every event of a relationship with every medication of the same48     subject's same relationship. */49  create table pairs as50    select e.STUDYID, e.USUBJID, e.AESEQ, m.CMSEQ, e.RELID51    from relae as e inner join relcm as m52      on m.STUDYID = e.STUDYID and m.USUBJID = e.USUBJID53         and m.RELID = e.RELID;54  /* The event's reported term. */55  create table aepairs as56    select p.STUDYID, p.USUBJID, p.AESEQ, a.AETERM, p.CMSEQ, p.RELID57    from pairs as p left join ae as a58      on a.STUDYID = p.STUDYID and a.USUBJID = p.USUBJID59         and a.AESEQ = p.AESEQ;60  /* The medication's reported name. */61  create table adaecm as62    select p.STUDYID, p.USUBJID, p.AESEQ, p.AETERM, p.CMSEQ, c.CMTRT,63           p.RELID64    from aepairs as p left join cm as c65      on c.STUDYID = p.STUDYID and c.USUBJID = p.USUBJID66         and c.CMSEQ = p.CMSEQ67    order by p.STUDYID, p.USUBJID, p.AESEQ, p.CMSEQ, p.RELID;68quit;6970proc export data=adaecm outfile='/app/output/adaecm.csv' dbms=csv replace; run;