Derive Investigator Overall Response Records

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

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

1# Reference solution for the yamaa benchmark adam-adrs-response-records (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(lubridate)9library(readr)10library(stringr)1112adsl <- read_csv(13  "/app/input/adsl.csv",14  col_types = cols(TRTSDT = col_date(), .default = col_character())15)16rs <- read_csv(17  "/app/input/rs.csv",18  col_types = cols(RSSEQ = col_integer(), .default = col_character())19)2021# Only investigator overall response assessments leave a record.22base <- rs |>23  filter(RSTESTCD %in% "OVRLRESP", RSEVAL %in% "INVESTIGATOR") |>24  left_join(select(adsl, USUBJID, TRTSDT), by = "USUBJID") |>25  mutate(26    PARAMCD = "OVR",27    PARAM = "Overall Response by Investigator",28    RSDTC = RSDTC,29    ADT = case_when(30      str_detect(RSDTC, "^[0-9]{4}-[0-9]{2}-[0-9]{2}$") ~ suppressWarnings(ymd(RSDTC, quiet = TRUE)),31      str_detect(RSDTC, "^[0-9]{4}-[0-9]{2}$") ~ suppressWarnings(ymd(paste0(RSDTC, "-01"), quiet = TRUE)),32      str_detect(RSDTC, "^[0-9]{4}$") ~ suppressWarnings(ymd(paste0(RSDTC, "-01-01"), quiet = TRUE)),33      .default = as.Date(NA)34    ),35    ADY = case_when(36      is.na(ADT) | is.na(TRTSDT) ~ NA_integer_,37      ADT >= TRTSDT ~ as.integer(ADT - TRTSDT) + 1L,38      .default = as.integer(ADT - TRTSDT)39    ),40    AVALC = RSSTRESC,41    AVAL = case_when(42      AVALC == "CR" ~ 1L,43      AVALC == "PR" ~ 2L,44      AVALC == "SD" ~ 3L,45      AVALC == "NON-CR/NON-PD" ~ 4L,46      AVALC == "PD" ~ 5L,47      AVALC == "NE" ~ 6L48    )49  )5051# One flagged record at each assessment date: the worst response that day,52# with the lowest sequence number breaking ties.53flagged <- base |>54  group_by(STUDYID, USUBJID, ADT) |>55  arrange(desc(AVAL), RSSEQ, .by_group = TRUE) |>56  mutate(57    rank = row_number(),58    ANL01FL = if_else(rank == 1L, "Y", NA_character_)59  ) |>60  ungroup() |>61  select(-rank)6263adrs <- flagged |>64  select(65    STUDYID, USUBJID, RSSEQ, PARAMCD, PARAM, RSDTC, ADT, ADY,66    AVALC, AVAL, ANL01FL67  ) |>68  arrange(USUBJID, ADT, RSSEQ)6970dir.create("/app/output", showWarnings = FALSE)71write_csv(adrs, "/app/output/adrs.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adrs-response-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 1.67"""Create ADRS (one record per investigator-scored overall response8assessment) from ADSL and RS, following CDISC ADaM standards."""910import csv11from datetime import date1213INPUT_DIR = "/app/input"14OUTPUT_DIR = "/app/output"1516AVAL_MAP = {17    "CR": 1,18    "PR": 2,19    "SD": 3,20    "NON-CR/NON-PD": 4,21    "PD": 5,22    "NE": 6,23}242526def complete_date(rsdtc):27    """Complete a possibly partial ISO date: a year and month without a28    day complete to the first of the month; a year alone completes to29    1 January."""30    parts = rsdtc.split("-")31    year = int(parts[0])32    month = int(parts[1]) if len(parts) > 1 else 133    day = int(parts[2]) if len(parts) > 2 else 134    return date(year, month, day)353637def parse_full_date(text):38    year, month, day = (int(p) for p in text.split("-"))39    return date(year, month, day)404142def main():43    with open(f"{INPUT_DIR}/adsl.csv", newline="") as f:44        adsl = {row["USUBJID"]: row for row in csv.DictReader(f)}4546    with open(f"{INPUT_DIR}/rs.csv", newline="") as f:47        rs_rows = list(csv.DictReader(f))4849    records = []50    for row in rs_rows:51        if row["RSTESTCD"] != "OVRLRESP" or row["RSEVAL"] != "INVESTIGATOR":52            continue53        trtsdt = parse_full_date(adsl[row["USUBJID"]]["TRTSDT"])54        adt = complete_date(row["RSDTC"])55        ady = (adt - trtsdt).days + 156        avalc = row["RSSTRESC"]57        records.append(58            {59                "STUDYID": row["STUDYID"],60                "USUBJID": row["USUBJID"],61                "RSSEQ": row["RSSEQ"],62                "PARAMCD": "OVR",63                "PARAM": "Overall Response by Investigator",64                "RSDTC": row["RSDTC"],65                "ADT": adt.isoformat(),66                "ADY": ady,67                "AVALC": avalc,68                "AVAL": AVAL_MAP[avalc],69                "ANL01FL": "",70            }71        )7273    # ANL01FL: one record per subject per assessment date (ADT) -- the74    # record carrying the worst response that day (largest AVAL), with75    # the lowest RSSEQ breaking ties.76    groups = {}77    for rec in records:78        key = (rec["USUBJID"], rec["ADT"])79        groups.setdefault(key, []).append(rec)80    for group in groups.values():81        flagged = min(group, key=lambda r: (-r["AVAL"], int(r["RSSEQ"])))82        flagged["ANL01FL"] = "Y"8384    fieldnames = [85        "STUDYID", "USUBJID", "RSSEQ", "PARAMCD", "PARAM", "RSDTC",86        "ADT", "ADY", "AVALC", "AVAL", "ANL01FL",87    ]88    with open(f"{OUTPUT_DIR}/adrs.csv", "w", newline="") as f:89        writer = csv.DictWriter(f, fieldnames=fieldnames)90        writer.writeheader()91        writer.writerows(records)929394if __name__ == "__main__":95    main()

1/* opensas reference solution for the yamaa benchmark adam-adrs-response-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 TRTSDT $1024;7  infile "/app/input/adsl.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. TRTSDT : $char1024.;9run;1011data rs;12  length STUDYID USUBJID RSTESTCD RSEVAL RSDTC RSSTRESC $1024;13  infile "/app/input/rs.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024. RSSEQ RSTESTCD : $char1024. RSEVAL : $char1024. RSDTC : $char1024. RSSTRESC : $char1024.;15run;1617proc sql; create table joined as select a.*,b.TRTSDT from rs as a left join adsl as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID where a.RSTESTCD='OVRLRESP' and a.RSEVAL='INVESTIGATOR'; quit;18data assessments;19  length PARAMCD $8 PARAM $40 ADT $10 AVALC $16;20  set joined; PARAMCD='OVR'; PARAM='Overall Response by Investigator';21  ADT=RSDTC;22  if lengthn(RSDTC)=7 then ADT=cats(RSDTC,'-01');23  if lengthn(RSDTC)=4 then ADT=cats(RSDTC,'-01-01');24  if not missing(ADT) and not missing(TRTSDT) then do;25    ADY=input(ADT,yymmdd10.)-input(TRTSDT,yymmdd10.); if ADY>=0 then ADY=ADY+1;26  end;27  AVALC=RSSTRESC; select(AVALC); when('CR') AVAL=1; when('PR') AVAL=2; when('SD') AVAL=3; when('NON-CR/NON-PD') AVAL=4; when('PD') AVAL=5; when('NE') AVAL=6; otherwise AVAL=.; end;28run;29proc sort data=assessments; by STUDYID USUBJID ADT descending AVAL RSSEQ; run;30data result; length ANL01FL $1; set assessments; by STUDYID USUBJID ADT; if first.ADT then ANL01FL='Y'; run;3132proc sql;33  create table final as select STUDYID, USUBJID, RSSEQ, PARAMCD, PARAM, RSDTC, ADT, ADY, AVALC, AVAL, ANL01FL from result;34quit;35proc export data=final outfile="/app/output/adrs.csv" dbms=csv replace; run;