Related Records

1library(yamaa)23relrec <- yamaa_domain("spec.yaml")$output4relrec

1import yamaa23relrec = yamaa.yamaa_domain("spec.yaml").output4relrec

1# Reference solution for the yamaa benchmark sdtm-relrec-links (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)9library(tidyr)1011ae <- read_csv(12  "/app/input/ae.csv",13  col_types = cols(.default = col_character())14)15cm <- read_csv(16  "/app/input/cm.csv",17  col_types = cols(.default = col_character())18)1920# A record naming two link identifiers contributes one row per identifier.21ae_rows <- ae |>22  pivot_longer(23    cols = c(AELNKID1, AELNKID2),24    values_to = "RELID"25  ) |>26  filter(!is.na(RELID) & trimws(RELID) != "") |>27  mutate(28    RDOMAIN = "AE",29    IDVAR = "AESEQ",30    IDVARVAL = trimws(AESEQ),31    # Link numbers as text without a decimal point.32    RELID = as.character(suppressWarnings(as.integer(RELID))),33    RELTYPE = NA_character_34  ) |>35  select(STUDYID, USUBJID, RDOMAIN, IDVAR, IDVARVAL, RELTYPE, RELID)3637cm_rows <- cm |>38  pivot_longer(39    cols = c(CMLNKID1, CMLNKID2),40    values_to = "RELID"41  ) |>42  filter(!is.na(RELID) & trimws(RELID) != "") |>43  mutate(44    RDOMAIN = "CM",45    IDVAR = "CMSEQ",46    IDVARVAL = trimws(CMSEQ),47    RELID = as.character(suppressWarnings(as.integer(RELID))),48    RELTYPE = NA_character_49  ) |>50  select(STUDYID, USUBJID, RDOMAIN, IDVAR, IDVARVAL, RELTYPE, RELID)5152relrec <- bind_rows(ae_rows, cm_rows) |>53  arrange(54    USUBJID, suppressWarnings(as.integer(RELID)), RDOMAIN,55    suppressWarnings(as.integer(IDVARVAL))56  ) |>57  select(STUDYID, USUBJID, RDOMAIN, IDVAR, IDVARVAL, RELTYPE, RELID)5859dir.create("/app/output", showWarnings = FALSE)60write_csv(relrec, "/app/output/relrec.csv", na = "")

1# Reference solution for the yamaa benchmark sdtm-relrec-links (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 pl101112def _present(value) -> bool:13    return value is not None and str(value).strip() != ""141516def _link(value) -> str | None:17    """A collected link number as text without a decimal point."""18    if not _present(value):19        return None20    text = str(value).strip()21    try:22        number = float(text)23        if number.is_integer():24            return str(int(number))25        return str(number)26    except ValueError:27        return text282930ae = pl.read_csv("/app/input/ae.csv", infer_schema=False)31cm = pl.read_csv("/app/input/cm.csv", infer_schema=False)3233rows = []34for row in ae.to_dicts():35    for link_col in ("AELNKID1", "AELNKID2"):36        relid = _link(row.get(link_col))37        # A record with no link identifier contributes no row.38        if relid is None:39            continue40        rows.append(41            {42                "STUDYID": row["STUDYID"],43                "USUBJID": row["USUBJID"],44                "RDOMAIN": "AE",45                "IDVAR": "AESEQ",46                "IDVARVAL": str(row["AESEQ"]).strip(),47                "RELTYPE": None,48                "RELID": relid,49            }50        )51for row in cm.to_dicts():52    for link_col in ("CMLNKID1", "CMLNKID2"):53        relid = _link(row.get(link_col))54        if relid is None:55            continue56        rows.append(57            {58                "STUDYID": row["STUDYID"],59                "USUBJID": row["USUBJID"],60                "RDOMAIN": "CM",61                "IDVAR": "CMSEQ",62                "IDVARVAL": str(row["CMSEQ"]).strip(),63                "RELTYPE": None,64                "RELID": relid,65            }66        )6768relrec = (69    pl.DataFrame(70        rows,71        schema={72            "STUDYID": pl.String,73            "USUBJID": pl.String,74            "RDOMAIN": pl.String,75            "IDVAR": pl.String,76            "IDVARVAL": pl.String,77            "RELTYPE": pl.String,78            "RELID": pl.String,79        },80    )81    .with_columns(82        pl.col("IDVARVAL").cast(pl.Int64).alias("_seq"),83        pl.col("RELID").cast(pl.Int64).alias("_rel"),84    )85    .sort(["USUBJID", "_rel", "RDOMAIN", "_seq"])86    .select("STUDYID", "USUBJID", "RDOMAIN", "IDVAR", "IDVARVAL", "RELTYPE", "RELID")87)8889Path("/app/output").mkdir(exist_ok=True)90relrec.write_csv("/app/output/relrec.csv")

1/* opensas reference solution for the yamaa benchmark sdtm-relrec-links.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 AELNKID1 AELNKID2 $1024;7  infile "/app/input/ae.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. AESEQ AETERM : $char1024. AELNKID1 : $char1024. AELNKID2 : $char1024.;9run;1011data cm;12  length STUDYID USUBJID CMTRT CMLNKID1 CMLNKID2 $1024;13  infile "/app/input/cm.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024. CMSEQ CMTRT : $char1024. CMLNKID1 : $char1024. CMLNKID2 : $char1024.;15run;1617data aelinks; set ae; length RDOMAIN IDVAR IDVARVAL RELTYPE RELID $1024; RDOMAIN='AE'; IDVAR='AESEQ'; IDVARVAL=strip(put(AESEQ,best32.)); RELTYPE='';18if not missing(AELNKID1) then do; RELID=AELNKID1; output; end;19if not missing(AELNKID2) then do; RELID=AELNKID2; output; end;20run;21data cmlinks; set cm; length RDOMAIN IDVAR IDVARVAL RELTYPE RELID $1024; RDOMAIN='CM'; IDVAR='CMSEQ'; IDVARVAL=strip(put(CMSEQ,best32.)); RELTYPE='';22if not missing(CMLNKID1) then do; RELID=CMLNKID1; output; end;23if not missing(CMLNKID2) then do; RELID=CMLNKID2; output; end;24run;25data result; set aelinks cmlinks; run;26proc sql;27  create table final as select STUDYID, USUBJID, RDOMAIN, IDVAR, IDVARVAL, RELTYPE, RELID from result;28quit;29proc export data=final outfile="/app/output/relrec.csv" dbms=csv replace; run;