Multiple Findings About from ODM

1library(yamaa)23fa <- yamaa_domain("spec.yaml")$output4fa

1import yamaa23fa = yamaa.yamaa_domain("spec.yaml").output4fa

1# Reference solution for the yamaa benchmark sdtm-fa-odm-multitest (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)9library(purrr)1011odm <- read_csv(12  "/app/input/odm.csv",13  col_types = cols(.default = col_character())14) |>15  mutate(Value = na_if(Value, ""))1617forms <- odm |>18  filter(ItemGroupOID == "IG.FA") |>19  distinct(20    StudyOID, SubjectKey, StudyEventOID, StudyEventRepeatKey,21    ItemGroupRepeatKey22  )2324one_form <- function(study, subj, event, rep, igrep) {25  sub <- odm |>26    filter(27      SubjectKey == subj,28      StudyEventOID == event,29      StudyEventRepeatKey == rep,30      ItemGroupOID == "IG.FA",31      ItemGroupRepeatKey == igrep32    )33  present <- sub$ItemOID34  get <- function(oid) {35    hit <- sub |> filter(ItemOID == oid)36    if (nrow(hit) == 0) return(list(present = FALSE, value = NA_character_))37    list(present = TRUE, value = hit$Value[[1]])38  }39  obj <- get("IT.FA.FAOBJ")40  if (!obj$present || is.na(obj$value)) return(tibble())41  fadtc <- get("IT.FA.FADTC")$value42  day <- dplyr::recode(event, DAY1 = 1L, DAY2 = 2L, .default = 99L)43  fatpt <- dplyr::recode(44    event, DAY1 = "END DAY 1", DAY2 = "END DAY 2", .default = NA_character_45  )46  specs <- list(47    list(oid = "IT.FA.OCCUR", code = "OCCUR", name = "Occurrence Indicator"),48    list(oid = "IT.FA.SEV", code = "SEV", name = "Severity/Intensity"),49    list(oid = "IT.FA.LDIAM", code = "LDIAM", name = "Longest Diameter")50  )51  imap_dfr(specs, function(spec, i) {52    g <- get(spec$oid)53    if (!g$present) return(tibble())54    blank <- is.na(g$value)55    tibble(56      DOMAIN = "FA",57      STUDYID = study,58      USUBJID = subj,59      DAY = day,60      REP = as.integer(igrep),61      ORDER = as.integer(i - 1L),62      FATESTCD = spec$code,63      FATEST = spec$name,64      FAOBJ = obj$value,65      FACAT = "REACTOGENICITY",66      FAORRES = g$value,67      FAORRESU = if_else(spec$oid == "IT.FA.LDIAM", "mm", NA_character_),68      FASTRESC = g$value,69      FASTAT = if_else(blank, "NOT DONE", NA_character_),70      FATPT = fatpt,71      FADTC = fadtc72    )73  })74}7576fa <- pmap_dfr(77  list(78    forms$StudyOID, forms$SubjectKey, forms$StudyEventOID,79    forms$StudyEventRepeatKey, forms$ItemGroupRepeatKey80  ),81  one_form82) |>83  arrange(STUDYID, USUBJID, DAY, REP, ORDER) |>84  group_by(STUDYID, USUBJID) |>85  mutate(FASEQ = row_number()) |>86  ungroup() |>87  select(88    DOMAIN, STUDYID, USUBJID, FASEQ, FATESTCD, FATEST, FAOBJ, FACAT,89    FAORRES, FAORRESU, FASTRESC, FASTAT, FATPT, FADTC90  )9192dir.create("/app/output", showWarnings = FALSE)93write_csv(fa, "/app/output/fa.csv", na = "")

1# Reference solution for the yamaa benchmark sdtm-fa-odm-multitest (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 pl1011odm = pl.read_csv("/app/input/odm.csv", infer_schema=False)1213forms = {}14study_of = {}15for r in odm.to_dicts():16    study_of[r["SubjectKey"]] = r["StudyOID"]17    if r["ItemGroupOID"] != "IG.FA":18        continue19    key = (20        r["SubjectKey"],21        r["StudyEventOID"],22        r["StudyEventRepeatKey"],23        r["ItemGroupRepeatKey"],24    )25    forms.setdefault(key, {})[r["ItemOID"]] = r["Value"]2627day_order = {"DAY1": 1, "DAY2": 2}28tpt_of = {"DAY1": "END DAY 1", "DAY2": "END DAY 2"}29test_order = {"IT.FA.OCCUR": 0, "IT.FA.SEV": 1, "IT.FA.LDIAM": 2}30test_info = {31    "IT.FA.OCCUR": ("OCCUR", "Occurrence Indicator"),32    "IT.FA.SEV": ("SEV", "Severity/Intensity"),33    "IT.FA.LDIAM": ("LDIAM", "Longest Diameter"),34}3536rows = []37for (subj, event, _rep, repkey), form in forms.items():38    obj = form.get("IT.FA.FAOBJ")39    fadtc = form.get("IT.FA.FADTC")40    if obj is None or obj == "":41        continue42    for oid in ("IT.FA.OCCUR", "IT.FA.SEV", "IT.FA.LDIAM"):43        if oid not in form:44            continue45        raw = form[oid]46        blank = raw is None or raw == ""47        val = None if blank else raw48        code, name = test_info[oid]49        rows.append(50            {51                "DOMAIN": "FA",52                "STUDYID": study_of[subj],53                "USUBJID": subj,54                "DAY": day_order.get(event, 99),55                "REP": int(repkey),56                "ORDER": test_order[oid],57                "FATESTCD": code,58                "FATEST": name,59                "FAOBJ": obj,60                "FACAT": "REACTOGENICITY",61                "FAORRES": val,62                "FAORRESU": "mm" if oid == "IT.FA.LDIAM" else None,63                "FASTRESC": val,64                "FASTAT": "NOT DONE" if blank else None,65                "FATPT": tpt_of.get(event),66                "FADTC": fadtc,67            }68        )6970fa = (71    pl.DataFrame(72        rows,73        schema={74            "DOMAIN": pl.String,75            "STUDYID": pl.String,76            "USUBJID": pl.String,77            "DAY": pl.Int64,78            "REP": pl.Int64,79            "ORDER": pl.Int64,80            "FATESTCD": pl.String,81            "FATEST": pl.String,82            "FAOBJ": pl.String,83            "FACAT": pl.String,84            "FAORRES": pl.String,85            "FAORRESU": pl.String,86            "FASTRESC": pl.String,87            "FASTAT": pl.String,88            "FATPT": pl.String,89            "FADTC": pl.String,90        },91    )92    .sort(["STUDYID", "USUBJID", "DAY", "REP", "ORDER"])93    .with_columns(94        pl.int_range(1, pl.len() + 1).over(["STUDYID", "USUBJID"]).alias("FASEQ")95    )96    .select(97        "DOMAIN",98        "STUDYID",99        "USUBJID",100        "FASEQ",101        "FATESTCD",102        "FATEST",103        "FAOBJ",104        "FACAT",105        "FAORRES",106        "FAORRESU",107        "FASTRESC",108        "FASTAT",109        "FATPT",110        "FADTC",111    )112)113114Path("/app/output").mkdir(parents=True, exist_ok=True)115fa.write_csv("/app/output/fa.csv")

1/* opensas reference solution for the yamaa benchmark sdtm-fa-odm-multitest.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data odm;6  length StudyOID MetaDataVersionOID SubjectKey StudyEventOID StudyEventRepeatKey ItemGroupOID ItemGroupRepeatKey ItemOID Value $1024;7  infile "/app/input/odm.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input StudyOID : $char1024. MetaDataVersionOID : $char1024. SubjectKey : $char1024. StudyEventOID : $char1024. StudyEventRepeatKey : $char1024. ItemGroupOID : $char1024. ItemGroupRepeatKey : $char1024. ItemOID : $char1024. Value : $char1024.;9run;1011proc sort data=odm out=ordered; by StudyOID SubjectKey StudyEventOID StudyEventRepeatKey ItemGroupRepeatKey; run;12data siblings;13  length FAOBJ FADTC $1024;14  retain FAOBJ FADTC;15  set ordered;16  where ItemGroupOID='IG.FA';17  by StudyOID SubjectKey StudyEventOID StudyEventRepeatKey ItemGroupRepeatKey;18  if first.ItemGroupRepeatKey then do;19    FAOBJ=''; FADTC='';20  end;21    if ItemOID='IT.FA.FAOBJ' then FAOBJ=Value;22  if ItemOID='IT.FA.FADTC' then FADTC=Value;23  if last.ItemGroupRepeatKey then output;24run;25proc sql;26create table joined as select a.*,b.FAOBJ,b.FADTC from odm a inner join siblings b on a.StudyOID=b.StudyOID and a.SubjectKey=b.SubjectKey and a.StudyEventOID=b.StudyEventOID and a.StudyEventRepeatKey=b.StudyEventRepeatKey and a.ItemGroupRepeatKey=b.ItemGroupRepeatKey where a.ItemOID in ('IT.FA.OCCUR','IT.FA.SEV','IT.FA.LDIAM'); quit;27data prepared; set joined; length DOMAIN $2 STUDYID USUBJID FATESTCD FATEST FACAT FAORRES FAORRESU FASTRESC FASTAT FATPT $1024;28DOMAIN='FA'; STUDYID=StudyOID; USUBJID=SubjectKey; FACAT='REACTOGENICITY'; FAORRES=Value; FASTRESC=Value; FAORRESU=''; FASTAT=''; if missing(Value) then FASTAT='NOT DONE';29if ItemOID='IT.FA.OCCUR' then do; FATESTCD='OCCUR'; FATEST='Occurrence Indicator'; TESTORD=1; end;30if ItemOID='IT.FA.SEV' then do; FATESTCD='SEV'; FATEST='Severity/Intensity'; TESTORD=2; end;31if ItemOID='IT.FA.LDIAM' then do; FATESTCD='LDIAM'; FATEST='Longest Diameter'; FAORRESU='mm'; TESTORD=3; end;32FATPT='END DAY 1'; if StudyEventOID='DAY2' then FATPT='END DAY 2'; DAYORD=input(compress(StudyEventOID,,'kd'),best32.); REP=input(ItemGroupRepeatKey,best32.); run;33proc sort data=prepared; by STUDYID USUBJID DAYORD REP TESTORD; run;34data result; set prepared; by STUDYID USUBJID; retain FASEQ;35  if first.USUBJID then FASEQ=0;36  FASEQ+1;37run;3839proc sql;40  create table final as select DOMAIN, STUDYID, USUBJID, FASEQ, FATESTCD, FATEST, FAOBJ, FACAT, FAORRES, FAORRESU, FASTRESC, FASTAT, FATPT, FADTC from result;41quit;42proc export data=final outfile="/app/output/fa.csv" dbms=csv replace; run;