Code Reported Terms Against a Medical Dictionary

1library(yamaa)23yamaa_project("project.yaml")$spec("AE")$run()$output

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

1# Reference solution for the yamaa benchmark sdtm-ae-coding (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_raw <- read_csv(11  "/app/input/ae_raw.csv",12  col_types = cols(AESEQ = col_integer(), .default = col_character())13)14meddra <- read_csv(15  "/app/input/meddra_26_1.csv",16  col_types = cols(.default = col_character())17)1819# The reported term in upper case, coded to the preferred term and body20# system of the entry whose lowest-level term, in upper case, equals it. A21# term with no match is not coded.22ae <- ae_raw |>23  mutate(AETERM = toupper(AETERM)) |>24  left_join(25    mutate(meddra, LLTNAME = toupper(LLTNAME)),26    by = c("AETERM" = "LLTNAME")27  ) |>28  mutate(29    DOMAIN = "AE",30    AEDECOD = if_else(is.na(PTNAME), "NOT CODED", PTNAME),31    AEBODSYS = if_else(is.na(SOCNAME), "NOT CODED", SOCNAME)32  ) |>33  select(DOMAIN, STUDYID, USUBJID, AESEQ, AETERM, AEDECOD, AEBODSYS)3435dir.create("/app/output", showWarnings = FALSE)36write_csv(ae, "/app/output/ae.csv", na = "")

1# Reference solution for the yamaa benchmark sdtm-ae-coding (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 1.67"""Create the SDTM AE dataset by coding reported terms against MedDRA 26.1.89Reads AE_RAW and MEDDRA_26_1 from /app/input and writes ae.csv to10/app/output with one record per adverse event. AETERM is stored in upper11case and matched to the dictionary's lowest-level term in upper case; the12preferred term and body system come from the matched entry. A term with13no match is coded "NOT CODED" in both fields.14"""1516import csv17from pathlib import Path1819INPUT = Path("/app/input")20OUTPUT = Path("/app/output")2122NOT_CODED = "NOT CODED"232425def read_rows(path):26    with open(path, newline="", encoding="utf-8") as handle:27        return list(csv.DictReader(handle))282930def main():31    dictionary = {}32    for entry in read_rows(INPUT / "meddra_26_1.csv"):33        dictionary[entry["LLTNAME"].upper()] = (entry["PTNAME"], entry["SOCNAME"])3435    records = []36    for event in read_rows(INPUT / "ae_raw.csv"):37        term = event["AETERM"].upper()38        if term in dictionary:39            decoded, body_system = dictionary[term]40        else:41            decoded, body_system = NOT_CODED, NOT_CODED42        records.append(43            {44                "DOMAIN": "AE",45                "STUDYID": event["STUDYID"],46                "USUBJID": event["USUBJID"],47                "AESEQ": event["AESEQ"],48                "AETERM": term,49                "AEDECOD": decoded,50                "AEBODSYS": body_system,51            }52        )5354    OUTPUT.mkdir(parents=True, exist_ok=True)55    columns = ["DOMAIN", "STUDYID", "USUBJID", "AESEQ", "AETERM", "AEDECOD", "AEBODSYS"]56    with open(OUTPUT / "ae.csv", "w", newline="", encoding="utf-8") as handle:57        writer = csv.DictWriter(handle, fieldnames=columns)58        writer.writeheader()59        writer.writerows(records)606162if __name__ == "__main__":63    main()

1/* opensas reference solution for the yamaa benchmark sdtm-ae-coding.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data ae_raw;6  length STUDYID USUBJID AETERM $1024;7  infile "/app/input/ae_raw.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. AESEQ AETERM : $char1024.;9run;1011data meddra_26_1;12  length LLTNAME PTNAME SOCNAME $1024;13  infile "/app/input/meddra_26_1.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input LLTNAME : $char1024. PTNAME : $char1024. SOCNAME : $char1024.;15run;1617proc sql;18  create table result as19  select 'AE' as DOMAIN,a.STUDYID,a.USUBJID,a.AESEQ,upcase(a.AETERM) as AETERM,coalescec(b.PTNAME,'NOT CODED') as AEDECOD,coalescec(b.SOCNAME,'NOT CODED') as AEBODSYS from ae_raw a left join meddra_26_1 b on upcase(a.AETERM)=upcase(b.LLTNAME);20quit;2122proc sql;23  create table final as select DOMAIN, STUDYID, USUBJID, AESEQ, AETERM, AEDECOD, AEBODSYS from result;24quit;25proc export data=final outfile="/app/output/ae.csv" dbms=csv replace; run;