Place each vital-signs record in its crossover period

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

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

1# Reference solution for the yamaa benchmark2# adam-advs-crossover-period-records (R track).3#4# Written from the benchmark's full prompt and its inputs alone, as an agent5# would write it. Harbor's oracle agent runs it to check that the prompt can6# be solved and that the grader scores a correct answer 1.78library(dplyr, warn.conflicts = FALSE)9library(lubridate)10library(readr)11library(stringr)1213vs <- read_csv(14  "/app/input/vs.csv",15  col_types = cols(16    VSSEQ = col_integer(), VSSTRESN = col_double(),17    .default = col_character()18  )19)20adsl <- read_csv(21  "/app/input/adsl.csv",22  col_types = cols(23    AP01SDT = col_date(), AP02SDT = col_date(),24    AP01SDTM = col_datetime(), AP02SDTM = col_datetime(),25    .default = col_character()26  )27)2829# The collection date is the date part of the collection datetime;30# the datetime itself exists only when a time was collected. A time31# may be written with or without seconds, so both forms are tried.32collected <- vs |>33  mutate(34    ADT = as.Date(str_sub(VSDTC, 1, 10)),35    parsed_hms = suppressWarnings(ymd_hms(VSDTC, quiet = TRUE, tz = "UTC")),36    parsed_hm = suppressWarnings(ymd_hm(VSDTC, quiet = TRUE, tz = "UTC")),37    moment = case_when(38      !is.na(VSDTC) & str_detect(VSDTC, "T") ~39        coalesce(parsed_hms, parsed_hm),40      .default = as.POSIXct(NA, tz = "UTC")41    ),42    ADTM = format(moment, "%Y-%m-%dT%H:%M:%S", tz = "UTC")43  )4445# The latest period whose start is at or before the record. A record46# with a time is compared with the period start datetimes, a date-only47# record with the period start dates; a missing start never matches,48# so a subject who never started period 2 stays in period 1.49advs <- collected |>50  left_join(adsl, by = c("STUDYID", "USUBJID")) |>51  mutate(52    APERIOD = case_when(53      !is.na(moment) & !is.na(AP02SDTM) & moment >= AP02SDTM ~ 2L,54      is.na(moment) & !is.na(ADT) & !is.na(AP02SDT) & ADT >= AP02SDT ~ 2L,55      !is.na(moment) & !is.na(AP01SDTM) & moment >= AP01SDTM ~ 1L,56      is.na(moment) & !is.na(ADT) & !is.na(AP01SDT) & ADT >= AP01SDT ~ 1L,57      .default = NA_integer_58    ),59    PARAMCD = VSTESTCD,60    AVAL = VSSTRESN,61    TRTA = case_when(62      APERIOD %in% 1L ~ TRT01A,63      APERIOD %in% 2L ~ TRT02A,64      .default = NA_character_65    )66  ) |>67  select(68    STUDYID, USUBJID, VSSEQ, PARAMCD, AVAL, ADT, ADTM, APERIOD, TRTA69  )7071dir.create("/app/output", showWarnings = FALSE)72write_csv(advs, "/app/output/advs.csv", na = "")

1# Reference solution for the yamaa benchmark adam-advs-crossover-period-records (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 1.67import csv8from datetime import datetime910INPUT_DIR = "/app/input"11OUTPUT_DIR = "/app/output"121314def parse_date(text):15    text = (text or "").strip()16    if not text:17        return None18    return datetime.strptime(text, "%Y-%m-%d").date()192021def parse_dtc(text):22    """Return (date, datetime or None) for an ISO 8601 collection value.2324    A date-only value yields a date with no datetime; a value carrying a25    time yields both its date and its datetime.26    """27    text = (text or "").strip()28    if not text:29        return None, None30    if "T" not in text:31        return parse_date(text), None32    for fmt in ("%Y-%m-%dT%H:%M:%S", "%Y-%m-%dT%H:%M"):33        try:34            moment = datetime.strptime(text, fmt)35            return moment.date(), moment36        except ValueError:37            continue38    raise ValueError("unrecognised datetime: %r" % text)394041def fmt_date(d):42    return d.isoformat() if d is not None else ""434445def fmt_dtm(m):46    return m.strftime("%Y-%m-%dT%H:%M:%S") if m is not None else ""474849def main():50    with open(INPUT_DIR + "/adsl.csv", newline="") as f:51        adsl = {row["USUBJID"]: row for row in csv.DictReader(f)}52    with open(INPUT_DIR + "/vs.csv", newline="") as f:53        vs_rows = list(csv.DictReader(f))5455    out_rows = []56    for row in vs_rows:57        subj = adsl[row["USUBJID"]]58        # Periods the subject started, in order: (number, start date,59        # start datetime, actual treatment).60        periods = []61        for num, sdt_key, sdtm_key, trt_key in (62            (1, "AP01SDT", "AP01SDTM", "TRT01A"),63            (2, "AP02SDT", "AP02SDTM", "TRT02A"),64        ):65            start_date = parse_date(subj.get(sdt_key))66            if start_date is None:67                continue68            _, start_dtm = parse_dtc(subj.get(sdtm_key))69            if start_dtm is None:70                start_dtm = datetime.combine(start_date, datetime.min.time())71            periods.append((num, start_date, start_dtm, subj.get(trt_key) or ""))7273        coll_date, coll_dtm = parse_dtc(row.get("VSDTC"))74        aperiod = ""75        trta = ""76        if coll_date is not None:77            for num, start_date, start_dtm, trt in periods:78                if coll_dtm is not None:79                    placed = start_dtm <= coll_dtm80                else:81                    placed = start_date <= coll_date82                if placed:83                    aperiod = num84                    trta = trt85        out_rows.append(86            {87                "STUDYID": row["STUDYID"],88                "USUBJID": row["USUBJID"],89                "VSSEQ": row["VSSEQ"],90                "PARAMCD": row["VSTESTCD"],91                "AVAL": row["VSSTRESN"],92                "ADT": fmt_date(coll_date),93                "ADTM": fmt_dtm(coll_dtm),94                "APERIOD": aperiod,95                "TRTA": trta,96            }97        )9899    fieldnames = [100        "STUDYID",101        "USUBJID",102        "VSSEQ",103        "PARAMCD",104        "AVAL",105        "ADT",106        "ADTM",107        "APERIOD",108        "TRTA",109    ]110    with open(OUTPUT_DIR + "/advs.csv", "w", newline="") as f:111        writer = csv.DictWriter(f, fieldnames=fieldnames)112        writer.writeheader()113        writer.writerows(out_rows)114115116if __name__ == "__main__":117    main()

1/* opensas reference solution for the yamaa benchmark adam-advs-crossover-period-records.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 TRT01A TRT02A AP01SDT AP01SDTM AP02SDT AP02SDTM $1024;7  infile "/app/input/adsl.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. TRT01A : $char1024. TRT02A : $char1024. AP01SDT : $char1024. AP01SDTM : $char1024. AP02SDT : $char1024. AP02SDTM : $char1024.;9run;1011data vs;12  length STUDYID USUBJID VSTESTCD VSDTC $1024;13  infile "/app/input/vs.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024. VSSEQ VSTESTCD : $char1024. VSSTRESN VSDTC : $char1024.;15run;1617/* The collection date is the date part of VSDTC. ADTM holds the full18   datetime, with seconds added when the collected time has none, and19   is empty when only a date was collected. ISO text compares in20   calendar and clock order. */21data collected;22  length PARAMCD $16 ADT ADTM $19;23  set vs;24  PARAMCD=VSTESTCD; AVAL=VSSTRESN;25  if not missing(VSDTC) then ADT=substr(VSDTC,1,10);26  if index(VSDTC,'T') then do;27    if length(trim(VSDTC))=16 then ADTM=trim(VSDTC)||":00";28    else ADTM=VSDTC;29  end;30run;3132proc sql;33  create table joined as select a.*,b.TRT01A,b.TRT02A,b.AP01SDT,b.AP01SDTM,b.AP02SDT,b.AP02SDTM from collected as a34    left join adsl as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID;35quit;3637/* The latest period whose start is at or before the record: a record38   with a time is compared with the start datetimes, a date-only39   record with the start dates, and a missing start never matches. */40data result;41  length TRTA $1024;42  set joined;43  if not missing(ADTM) and not missing(AP02SDTM) and ADTM>=AP02SDTM then APERIOD=2;44  else if missing(ADTM) and not missing(ADT) and not missing(AP02SDT) and ADT>=AP02SDT then APERIOD=2;45  else if not missing(ADTM) and not missing(AP01SDTM) and ADTM>=AP01SDTM then APERIOD=1;46  else if missing(ADTM) and not missing(ADT) and not missing(AP01SDT) and ADT>=AP01SDT then APERIOD=1;47  if APERIOD=1 then TRTA=TRT01A;48  else if APERIOD=2 then TRTA=TRT02A;49run;5051proc sql;52  create table final as select STUDYID, USUBJID, VSSEQ, PARAMCD, AVAL, ADT, ADTM, APERIOD, TRTA from result;53quit;54proc export data=final outfile="/app/output/advs.csv" dbms=csv replace; run;