Study Eye Flag

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

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

1# Reference solution for the yamaa benchmark adam-adoe-study-eye (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)910adsl <- read_csv(11  "/app/input/adsl.csv",12  col_types = cols(.default = col_character())13)14oe <- read_csv(15  "/app/input/oe.csv",16  col_types = cols(17    OESEQ = col_integer(),18    OESTRESN = col_double(),19    .default = col_character()20  )21)2223# The assigned eye belongs to the subject, so the join is by subject; a24# subject without an assigned eye keeps its measurements with no role.25adoe <- oe |>26  left_join(select(adsl, USUBJID, STUDYEYE), by = "USUBJID") |>27  mutate(28    PARAMCD = OETESTCD,29    AVAL = OESTRESN,30    AFEYE = case_when(31      is.na(STUDYEYE) | STUDYEYE == "" ~ NA_character_,32      is.na(OELAT) | OELAT == "" ~ NA_character_,33      OELAT == "BILATERAL" ~ "Both Eyes",34      STUDYEYE == "BILATERAL" ~ "Study Eye",35      OELAT == STUDYEYE ~ "Study Eye",36      .default = "Fellow Eye"37    )38  ) |>39  select(STUDYID, USUBJID, OESEQ, PARAMCD, OELAT, AVAL, AFEYE) |>40  arrange(USUBJID, OESEQ)4142dir.create("/app/output", showWarnings = FALSE)43write_csv(adoe, "/app/output/adoe.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adoe-study-eye (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 ADOE from ADSL and OE.89One record per collected ophthalmic examination measurement. AFEYE gives10the eye's role in the study, derived from the collected laterality11(OELAT) and the subject's assigned eye (STUDYEYE in ADSL):1213- "Both Eyes" for a bilateral measurement when the subject has an14  assigned eye.15- "Study Eye" when the measured eye matches the assigned eye; when the16  assigned eye is both eyes, a measurement of either eye is "Study Eye"17  whenever the collected laterality is present.18- "Fellow Eye" when the measured eye is the opposite eye to the19  assigned eye.20- No value when the subject has no assigned eye or the collected21  laterality is missing.2223A measurement collected without a value is kept with AVAL missing.24"""2526import csv27import os2829INPUT_DIR = "/app/input"30OUTPUT_DIR = "/app/output"313233def read_csv(path):34    with open(path, newline="", encoding="utf-8") as handle:35        return list(csv.DictReader(handle))363738def afeye(study_eye, oelat):39    if not study_eye or not oelat:40        return ""41    if oelat == "BILATERAL":42        return "Both Eyes"43    if study_eye == "BILATERAL":44        return "Study Eye"45    if oelat == study_eye:46        return "Study Eye"47    return "Fellow Eye"484950def main():51    adsl = read_csv(os.path.join(INPUT_DIR, "adsl.csv"))52    oe = read_csv(os.path.join(INPUT_DIR, "oe.csv"))5354    study_eye_by_subject = {55        (row["STUDYID"], row["USUBJID"]): row["STUDYEYE"] for row in adsl56    }5758    columns = ["STUDYID", "USUBJID", "OESEQ", "PARAMCD", "OELAT", "AVAL", "AFEYE"]59    records = []60    for row in oe:61        key = (row["STUDYID"], row["USUBJID"])62        records.append(63            {64                "STUDYID": row["STUDYID"],65                "USUBJID": row["USUBJID"],66                "OESEQ": row["OESEQ"],67                "PARAMCD": row["OETESTCD"],68                "OELAT": row["OELAT"],69                "AVAL": row["OESTRESN"],70                "AFEYE": afeye(study_eye_by_subject.get(key, ""), row["OELAT"]),71            }72        )7374    os.makedirs(OUTPUT_DIR, exist_ok=True)75    with open(76        os.path.join(OUTPUT_DIR, "adoe.csv"), "w", newline="", encoding="utf-8"77    ) as handle:78        writer = csv.DictWriter(handle, fieldnames=columns)79        writer.writeheader()80        writer.writerows(records)818283if __name__ == "__main__":84    main()

1/* opensas reference solution for the yamaa benchmark adam-adoe-study-eye.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data adsl;6  length STUDYID USUBJID STUDYEYE $1024;7  infile "/app/input/adsl.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. STUDYEYE : $char1024.;9run;1011data oe;12  length STUDYID USUBJID OETESTCD OELAT $1024;13  infile "/app/input/oe.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024. OESEQ OETESTCD : $char1024. OELAT : $char1024. OESTRESN;15run;1617proc sql;18  create table result as19  select a.*,a.OETESTCD as PARAMCD,a.OESTRESN as AVAL,case when missing(a.OELAT) or missing(b.STUDYEYE) then '' when a.OELAT='BILATERAL' then 'Both Eyes' when b.STUDYEYE='BILATERAL' or a.OELAT=b.STUDYEYE then 'Study Eye' else 'Fellow Eye' end as AFEYE from oe as a left join adsl as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID;20quit;2122proc sql;23  create table final as select STUDYID, USUBJID, OESEQ, PARAMCD, OELAT, AVAL, AFEYE from result;24quit;25proc export data=final outfile="/app/output/adoe.csv" dbms=csv replace; run;