Derive Investigator Overall Response Records

1library(yamaa)23adrs <- yamaa_domain("spec.yaml")$output4adrs

1import yamaa23adrs = yamaa.yamaa_domain("spec.yaml").output4adrs

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 1.67from pathlib import Path89import polars as pl1011adsl = pl.read_csv("/app/input/adsl.csv", infer_schema=False).with_columns(12    pl.col("TRTSDT").str.to_date()13)14rs = pl.read_csv("/app/input/rs.csv", infer_schema=False).with_columns(15    pl.col("RSSEQ").cast(pl.Int64)16)1718# Only investigator overall response assessments leave a record.19base = rs.filter(20    (pl.col("RSTESTCD") == "OVRLRESP") & (pl.col("RSEVAL") == "INVESTIGATOR")21).join(adsl.select("USUBJID", "TRTSDT"), on="USUBJID", how="left")2223full = pl.col("RSDTC").str.contains(r"^\d{4}-\d{2}-\d{2}$")24year_month = pl.col("RSDTC").str.contains(r"^\d{4}-\d{2}$")25year_only = pl.col("RSDTC").str.contains(r"^\d{4}$")2627# A completed date counts exactly as a collected one in every comparison.28adt = (29    pl.when(full)30    .then(pl.col("RSDTC").str.to_date(strict=False))31    .when(year_month)32    .then((pl.col("RSDTC") + "-01").str.to_date(strict=False))33    .when(year_only)34    .then((pl.col("RSDTC") + "-01-01").str.to_date(strict=False))35)3637ady = (38    pl.when(pl.col("ADT").is_null() | pl.col("TRTSDT").is_null())39    .then(None)40    .when(pl.col("ADT") >= pl.col("TRTSDT"))41    .then((pl.col("ADT") - pl.col("TRTSDT")).dt.total_days() + 1)42    .otherwise((pl.col("ADT") - pl.col("TRTSDT")).dt.total_days())43)4445derived = (46    base.with_columns(47        PARAMCD=pl.lit("OVR"),48        PARAM=pl.lit("Overall Response by Investigator"),49        ADT=adt,50    )51    .with_columns(52        ADY=ady.cast(pl.Int64),53        AVALC=pl.col("RSSTRESC"),54        AVAL=pl.col("RSSTRESC").replace_strict(55            {"CR": 1, "PR": 2, "SD": 3, "NON-CR/NON-PD": 4, "PD": 5, "NE": 6},56            default=None,57            return_dtype=pl.Int64,58        ),59    )60)6162# One flagged record at each assessment date: the worst response that day,63# with the lowest sequence number breaking ties.64ranked = derived.sort(65    ["STUDYID", "USUBJID", "ADT", "AVAL", "RSSEQ"],66    descending=[False, False, False, True, False],67).with_columns(68    rank=pl.col("RSSEQ").cum_count().over(["STUDYID", "USUBJID", "ADT"])69)7071adrs = (72    ranked.with_columns(73        ANL01FL=pl.when(pl.col("rank") == 1).then(pl.lit("Y")).otherwise(None)74    )75    .select(76        "STUDYID", "USUBJID", "RSSEQ", "PARAMCD", "PARAM", "RSDTC",77        "ADT", "ADY", "AVALC", "AVAL", "ANL01FL",78    )79    .sort(["USUBJID", "ADT", "RSSEQ"])80)8182Path("/app/output").mkdir(exist_ok=True)83adrs.write_csv("/app/output/adrs.csv")

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;