Set below-limit concentrations by their place in the profile

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

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

1# Reference solution for the yamaa benchmark adam-adpc-blq-imputation (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)910pc <- read_csv(11  "/app/input/pc.csv",12  col_types = cols(13    PCSEQ = col_integer(),14    PCSTRESN = col_double(),15    PCTPTNUM = col_double(),16    .default = col_character()17  ),18  na = ""19)2021# The first and last quantified time points of each profile. A result22# below the limit and a sample not done have no number, so neither moves23# the quantified span.24span <- pc |>25  filter(!is.na(PCSTRESN)) |>26  group_by(STUDYID, USUBJID, PCTESTCD, PCTPTREF) |>27  summarise(28    FIRSTQ = min(PCTPTNUM),29    LASTQ = max(PCTPTNUM),30    .groups = "drop"31  )3233based <- pc |>34  left_join(35    span,36    by = c("STUDYID", "USUBJID", "PCTESTCD", "PCTPTREF")37  )3839# A quantified result as recorded; a below-limit result is 0 before the40# first or after the last quantified result of its profile (and in a41# profile with no quantified result), and has no value between them. A42# sample not done has no value.43adpc <- based |>44  mutate(45    AVAL = case_when(46      !is.na(PCSTRESN) ~ PCSTRESN,47      !is.na(PCSTRESC) & startsWith(PCSTRESC, "<") &48        (is.na(FIRSTQ) | PCTPTNUM < FIRSTQ | PCTPTNUM > LASTQ) ~ 0,49      .default = NA_real_50    )51  ) |>52  select(53    STUDYID, USUBJID, PCSEQ,54    PARAMCD = PCTESTCD, ATPTREF = PCTPTREF, ATPT = PCTPT,55    ATPTN = PCTPTNUM, AVAL, AVALU = PCSTRESU56  )5758dir.create("/app/output", showWarnings = FALSE)59write_csv(adpc, "/app/output/adpc.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adpc-blq-imputation (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"""Build ADPC from PC with BLQ imputation.89One record per sample. AVAL is the quantified concentration as recorded;10a below-limit result ("<...") is 0 before the first or after the last11quantified result of its profile (subject, analyte, dose), and blank12between them. A not-done sample has no AVAL and neither starts nor ends13the quantified span.14"""1516import csv17from pathlib import Path1819INPUT = Path("/app/input")20OUTPUT = Path("/app/output")212223def main() -> None:24    with (INPUT / "pc.csv").open(newline="") as f:25        rows = list(csv.DictReader(f))2627    # Classify each sample.28    for r in rows:29        stat = (r.get("PCSTAT") or "").strip()30        stresc = (r.get("PCSTRESC") or "").strip()31        if stat == "NOT DONE" or stresc == "":32            r["_kind"] = "notdone"33        elif stresc.startswith("<"):34            r["_kind"] = "blq"35        else:36            r["_kind"] = "quant"3738    # Profiles: one subject, one analyte, one dose, in planned time order.39    profiles = {}40    for r in rows:41        key = (r["USUBJID"], r["PCTESTCD"], r["PCTPTREF"])42        profiles.setdefault(key, []).append(r)43    for members in profiles.values():44        members.sort(key=lambda r: (float(r["PCTPTNUM"]), int(r["PCSEQ"])))45        quant_pos = [i for i, r in enumerate(members) if r["_kind"] == "quant"]46        for i, r in enumerate(members):47            if r["_kind"] == "quant":48                r["_aval"] = (r.get("PCSTRESN") or "").strip()49            elif r["_kind"] == "blq":50                if not quant_pos or i < quant_pos[0] or i > quant_pos[-1]:51                    r["_aval"] = "0"52                else:53                    r["_aval"] = ""54            else:55                r["_aval"] = ""5657    out_fields = [58        "STUDYID", "USUBJID", "PCSEQ", "PARAMCD", "ATPTREF",59        "ATPT", "ATPTN", "AVAL", "AVALU",60    ]61    OUTPUT.mkdir(parents=True, exist_ok=True)62    with (OUTPUT / "adpc.csv").open("w", newline="") as f:63        w = csv.DictWriter(f, fieldnames=out_fields)64        w.writeheader()65        for r in rows:66            w.writerow({67                "STUDYID": r["STUDYID"],68                "USUBJID": r["USUBJID"],69                "PCSEQ": r["PCSEQ"],70                "PARAMCD": r["PCTESTCD"],71                "ATPTREF": r["PCTPTREF"],72                "ATPT": r["PCTPT"],73                "ATPTN": r["PCTPTNUM"],74                "AVAL": r["_aval"],75                "AVALU": "ng/mL",76            })777879if __name__ == "__main__":80    main()

1/* opensas reference solution for the yamaa benchmark adam-adpc-blq-imputation.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data pc;6  length STUDYID DOMAIN USUBJID PCTESTCD PCTEST PCORRES PCORRESU PCSTRESC PCSTRESU PCSTAT PCDTC PCTPT PCTPTREF PCRFTDTC $1024;7  infile "/app/input/pc.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. DOMAIN : $char1024. USUBJID : $char1024. PCSEQ PCTESTCD : $char1024. PCTEST : $char1024. PCORRES : $char1024. PCORRESU : $char1024. PCSTRESC : $char1024. PCSTRESN PCSTRESU : $char1024. PCSTAT : $char1024. PCLLOQ PCDTC : $char1024. PCTPT : $char1024. PCTPTNUM PCTPTREF : $char1024. PCRFTDTC : $char1024.;9run;1011/* The quantified samples only: a result below the limit and a sample not12   done have no number, so neither moves the quantified span. */13data quant;14  set pc;15  if not missing(PCSTRESN);16  keep STUDYID USUBJID PCTESTCD PCTPTREF PCTPTNUM;17run;1819proc sql;20  create table span as21    select STUDYID, USUBJID, PCTESTCD, PCTPTREF,22           min(PCTPTNUM) as FIRSTQ, max(PCTPTNUM) as LASTQ23    from quant24    group by STUDYID, USUBJID, PCTESTCD, PCTPTREF;25quit;2627proc sql;28  create table joined as29    select a.*, s.FIRSTQ, s.LASTQ30    from pc as a left join span as s31      on a.STUDYID = s.STUDYID and a.USUBJID = s.USUBJID32      and a.PCTESTCD = s.PCTESTCD and a.PCTPTREF = s.PCTPTREF;33quit;3435/* A quantified result as recorded; a below-limit result is 0 before the36   first or after the last quantified result of its profile (and in a37   profile with no quantified result), and has no value between them. */38data result;39  set joined;40  PARAMCD = PCTESTCD;41  ATPTREF = PCTPTREF;42  ATPT = PCTPT;43  ATPTN = PCTPTNUM;44  AVALU = PCSTRESU;45  if not missing(PCSTRESN) then AVAL = PCSTRESN;46  else if substr(PCSTRESC, 1, 1) = '<' and (missing(FIRSTQ) or PCTPTNUM < FIRSTQ or PCTPTNUM > LASTQ) then AVAL = 0;47  else AVAL = .;48run;4950proc sql;51  create table final as select STUDYID, USUBJID, PCSEQ, PARAMCD, ATPTREF, ATPT, ATPTN, AVAL, AVALU from result;52quit;53proc export data=final outfile="/app/output/adpc.csv" dbms=csv replace; run;