Ordered Float Sum

1library(yamaa)23adlb <- yamaa_domain("spec.yaml")$output4adlb

1import yamaa23adlb = yamaa.yamaa_domain("spec.yaml").output4adlb

1# Reference solution for the yamaa benchmark adam-adlb-ordered-sum (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)910lb <- read_csv(11  "/app/input/lb.csv",12  col_types = cols(13    LBSEQ = col_integer(),14    LBSTRESN = col_double(),15    .default = col_character()16  )17)1819# Keep every collected component record; DTYPE has no value on these.20components <- lb |>21  transmute(22    STUDYID, USUBJID,23    PARAMCD = LBTESTCD,24    PARAM = LBTEST,25    AVISIT = VISIT,26    AVAL = LBSTRESN,27    DTYPE = NA_character_28  )2930# One total record per subject and visit: the sum of the collected31# component results in laboratory sequence order. No value, rather than32# zero, when none of them has a collected result.33ordered_sum <- function(x) {34  vals <- x[!is.na(x)]35  if (length(vals) == 0) {36    return(NA_real_)37  }38  total <- vals[[1]]39  if (length(vals) > 1) {40    for (v in vals[-1]) {41      total <- total + v42    }43  }44  total45}4647totals <- lb |>48  arrange(USUBJID, VISIT, LBSEQ) |>49  group_by(STUDYID, USUBJID, VISIT) |>50  summarise(51    AVAL = ordered_sum(LBSTRESN),52    .groups = "drop"53  ) |>54  mutate(55    PARAMCD = "TOTAL",56    PARAM = "Total of Components",57    AVISIT = VISIT,58    DTYPE = "CALCULATION"59  ) |>60  select(STUDYID, USUBJID, PARAMCD, PARAM, AVISIT, AVAL, DTYPE)6162adlb <- bind_rows(components, totals)6364dir.create("/app/output", showWarnings = FALSE)65write_csv(adlb, "/app/output/adlb.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adlb-ordered-sum (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 pl1011lb = pl.read_csv("/app/input/lb.csv", infer_schema=False).with_columns(12    pl.col("LBSEQ").cast(pl.Int64),13    pl.col("LBSTRESN").cast(pl.Float64, strict=False).alias("AVAL"),14)1516# Keep every collected component record; DTYPE has no value on these.17components = lb.select(18    "STUDYID",19    "USUBJID",20    pl.col("LBTESTCD").alias("PARAMCD"),21    pl.col("LBTEST").alias("PARAM"),22    pl.col("VISIT").alias("AVISIT"),23    "AVAL",24    pl.lit(None, dtype=pl.String).alias("DTYPE"),25)262728# One total record per subject and visit: the sum of the collected29# component results in laboratory sequence order. No value, rather than30# zero, when none of them has a collected result.31def ordered_sum(values: list) -> float | None:32    nums = [v for v in values if v is not None]33    if not nums:34        return None35    total = nums[0]36    for value in nums[1:]:37        total = total + value38    return total394041totals = (42    lb.sort(["USUBJID", "VISIT", "LBSEQ"])43    .group_by("STUDYID", "USUBJID", "VISIT", maintain_order=True)44    .agg(pl.col("AVAL").alias("VALS"))45    .with_columns(46        PARAMCD=pl.lit("TOTAL"),47        PARAM=pl.lit("Total of Components"),48        AVISIT=pl.col("VISIT"),49        AVAL=pl.col("VALS").map_elements(50            ordered_sum, return_dtype=pl.Float6451        ),52        DTYPE=pl.lit("CALCULATION"),53    )54    .select("STUDYID", "USUBJID", "PARAMCD", "PARAM", "AVISIT", "AVAL", "DTYPE")55)5657adlb = pl.concat([components, totals], how="diagonal")5859Path("/app/output").mkdir(exist_ok=True)60adlb.write_csv("/app/output/adlb.csv")

1/* opensas reference solution for the yamaa benchmark adam-adlb-ordered-sum.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data lb;6  length STUDYID USUBJID LBTESTCD LBTEST VISIT $1024;7  infile "/app/input/lb.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. LBSEQ LBTESTCD : $char1024. LBTEST : $char1024. VISIT : $char1024. LBSTRESN;9run;1011data collected;12  length PARAMCD $16 PARAM $1024 AVISIT $1024 DTYPE $11;13  set lb; PARAMCD=LBTESTCD; PARAM=LBTEST; AVISIT=VISIT; AVAL=LBSTRESN;14run;15proc sort data=collected; by STUDYID USUBJID AVISIT LBSEQ; run;16data totals;17  length PARAMCD $16 PARAM $1024 DTYPE $11;18  set collected; by STUDYID USUBJID AVISIT;19  if first.AVISIT then do; total=0; count=0; end;20  if not missing(AVAL) then do; total+AVAL; count+1; end;21  if last.AVISIT then do;22    PARAMCD='TOTAL'; PARAM='Total of Components'; DTYPE='CALCULATION';23    AVAL=.; if count>0 then AVAL=total;24    output;25  end;26run;27data result; set collected totals; run;2829proc sql;30  create table final as select STUDYID, USUBJID, PARAMCD, PARAM, AVISIT, AVAL, DTYPE from result;31quit;32proc export data=final outfile="/app/output/adlb.csv" dbms=csv replace; run;