Subject elements from DM and an ODM extract

1library(yamaa)23se <- yamaa_domain("spec.yaml")$output4se

1import yamaa23se = yamaa.yamaa_domain("spec.yaml").output4se

1# Reference solution for the yamaa benchmark sdtm-se-subject-elements (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(tidyr)1011dm <- read_csv(12  "/app/input/dm.csv",13  col_types = cols(.default = col_character())14)15odm <- read_csv(16  "/app/input/odm.csv",17  col_types = cols(.default = col_character())18)1920wide <- odm |>21  mutate(Value = na_if(Value, "")) |>22  pivot_wider(23    id_cols = c(SubjectKey, StudyEventOID),24    names_from = ItemOID,25    values_from = Value,26    values_fn = function(x) x[[1]]27  )2829study_day <- function(ref, day) {30  ifelse(31    is.na(ref) | ref == "" | is.na(day) | day == "",32    NA_character_,33    {34      delta <- as.integer(as.Date(day) - as.Date(ref))35      as.character(ifelse(delta >= 0, delta + 1L, delta))36    }37  )38}3940se <- wide |>41  left_join(dm, by = c("SubjectKey" = "USUBJID")) |>42  mutate(43    DOMAIN = "SE",44    STUDYID = STUDYID,45    USUBJID = SubjectKey,46    SESEQ = IT.TA.TAETORD,47    ETCD = StudyEventOID,48    ELEMENT = IT.TE.ELEMENT,49    TAETORD = IT.TA.TAETORD,50    EPOCH = IT.TA.EPOCH,51    first_dtc = IT.EX.FIRSTDTC,52    last_dtc = IT.EX.LASTDTC,53    SESTDTC = case_when(54      EPOCH == "SCREENING" ~ RFICDTC,55      EPOCH == "TREATMENT" ~ first_dtc,56      TRUE ~ last_dtc57    ),58    SEENDTC = case_when(59      EPOCH == "SCREENING" ~ first_dtc,60      EPOCH == "TREATMENT" ~ last_dtc,61      TRUE ~ RFPENDTC62    ),63    SESTDY = study_day(RFSTDTC, SESTDTC),64    SEENDY = study_day(RFSTDTC, SEENDTC),65    SEUPDES = NA_character_66  ) |>67  arrange(USUBJID, suppressWarnings(as.integer(TAETORD))) |>68  select(69    DOMAIN, STUDYID, USUBJID, SESEQ, ETCD, ELEMENT, TAETORD, EPOCH,70    SESTDTC, SEENDTC, SESTDY, SEENDY, SEUPDES71  )7273dir.create("/app/output", showWarnings = FALSE)74write_csv(se, "/app/output/se.csv", na = "")

1# Reference solution for the yamaa benchmark sdtm-se-subject-elements (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 datetime import date8from pathlib import Path910import polars as pl111213def _present(value) -> bool:14    return value is not None and str(value) != ""151617def _parse(value) -> date | None:18    if not _present(value):19        return None20    return date.fromisoformat(str(value))212223def _study_day(ref: date | None, day: date | None) -> str | None:24    if ref is None or day is None:25        return None26    delta = (day - ref).days27    return str(delta + 1 if delta >= 0 else delta)282930dm = pl.read_csv("/app/input/dm.csv", infer_schema=False)31odm = pl.read_csv("/app/input/odm.csv", infer_schema=False)3233# Planned element per study event, and dosing dates per subject.34elements: dict[tuple, dict] = {}35dosing: dict[str, dict] = {}36for row in odm.to_dicts():37    subj = str(row["SubjectKey"])38    event = str(row["StudyEventOID"])39    oid, value = str(row["ItemOID"]), row["Value"]40    if oid == "IT.TE.ELEMENT":41        elements.setdefault((subj, event), {})["element"] = str(value)42    elif oid == "IT.TA.TAETORD":43        elements.setdefault((subj, event), {})["order"] = str(value)44    elif oid == "IT.TA.EPOCH":45        elements.setdefault((subj, event), {})["epoch"] = str(value)46    elif oid == "IT.EX.FIRSTDTC":47        dosing.setdefault(subj, {})["first"] = str(value) if _present(value) else None48    elif oid == "IT.EX.LASTDTC":49        dosing.setdefault(subj, {})["last"] = str(value) if _present(value) else None5051dm_by_subj = {str(r["USUBJID"]): r for r in dm.to_dicts()}5253rows = []54for (subj, etcd), info in elements.items():55    subject = dm_by_subj.get(subj)56    if subject is None:57        continue58    studyid = str(subject["STUDYID"])59    usubjid = str(subject["USUBJID"])60    epoch = info.get("epoch")61    order = info.get("order")62    first = (dosing.get(subj) or {}).get("first")63    last = (dosing.get(subj) or {}).get("last")64    rfic = str(subject.get("RFICDTC") or "")65    rfic = rfic if _present(rfic) else None66    rfstd = str(subject.get("RFSTDTC") or "")67    rfstd = rfstd if _present(rfstd) else None68    rfpen = str(subject.get("RFPENDTC") or "")69    rfpen = rfpen if _present(rfpen) else None70    if epoch == "SCREENING":71        stdtc, endtc = rfic, first72    elif epoch == "TREATMENT":73        stdtc, endtc = first, last74    else:75        # Follow-up, and any other or missing epoch.76        stdtc, endtc = last, rfpen77    ref = _parse(rfstd)78    rows.append(79        {80            "DOMAIN": "SE",81            "STUDYID": studyid,82            "USUBJID": usubjid,83            "SESEQ": order,84            "ETCD": etcd,85            "ELEMENT": info.get("element"),86            "TAETORD": order,87            "EPOCH": epoch,88            "SESTDTC": stdtc,89            "SEENDTC": endtc,90            "SESTDY": _study_day(ref, _parse(stdtc)),91            "SEENDY": _study_day(ref, _parse(endtc)),92            "SEUPDES": None,93        }94    )9596rows.sort(key=lambda r: (r["USUBJID"], int(r["TAETORD"] or 0)))9798se = (99    pl.DataFrame(100        rows,101        schema={102            "DOMAIN": pl.String,103            "STUDYID": pl.String,104            "USUBJID": pl.String,105            "SESEQ": pl.String,106            "ETCD": pl.String,107            "ELEMENT": pl.String,108            "TAETORD": pl.String,109            "EPOCH": pl.String,110            "SESTDTC": pl.String,111            "SEENDTC": pl.String,112            "SESTDY": pl.String,113            "SEENDY": pl.String,114            "SEUPDES": pl.String,115        },116    )117    .sort(["USUBJID", "TAETORD"])118    .select(119        "DOMAIN", "STUDYID", "USUBJID", "SESEQ", "ETCD", "ELEMENT", "TAETORD",120        "EPOCH", "SESTDTC", "SEENDTC", "SESTDY", "SEENDY", "SEUPDES",121    )122)123124Path("/app/output").mkdir(exist_ok=True)125se.write_csv("/app/output/se.csv")

1/* opensas reference solution for the yamaa benchmark sdtm-se-subject-elements.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data dm;6  length STUDYID USUBJID ARMCD RFICDTC RFSTDTC RFPENDTC $1024;7  infile "/app/input/dm.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. ARMCD : $char1024. RFICDTC : $char1024. RFSTDTC : $char1024. RFPENDTC : $char1024.;9run;1011data odm;12  length StudyOID MetaDataVersionOID SubjectKey StudyEventOID StudyEventRepeatKey ItemGroupOID ItemGroupRepeatKey ItemOID Value $1024;13  infile "/app/input/odm.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input StudyOID : $char1024. MetaDataVersionOID : $char1024. SubjectKey : $char1024. StudyEventOID : $char1024. StudyEventRepeatKey : $char1024. ItemGroupOID : $char1024. ItemGroupRepeatKey : $char1024. ItemOID : $char1024. Value : $char1024.;15run;1617proc sort data=odm out=ordered; by StudyOID SubjectKey StudyEventOID; run;18data elements;19  length ELEMENT ORD EPOCH $1024;20  retain ELEMENT ORD EPOCH;21  set ordered;2223  by StudyOID SubjectKey StudyEventOID;24  if first.StudyEventOID then do;25    ELEMENT=''; ORD=''; EPOCH='';26  end;27    if ItemOID='IT.TE.ELEMENT' then ELEMENT=Value;28  if ItemOID='IT.TA.TAETORD' then ORD=Value;29  if ItemOID='IT.TA.EPOCH' then EPOCH=Value;30  if last.StudyEventOID then output;31run;32proc sort data=odm out=ordered; by StudyOID SubjectKey; run;33data dosing;34  length FIRSTDTC LASTDTC $1024;35  retain FIRSTDTC LASTDTC;36  set ordered;3738  by StudyOID SubjectKey;39  if first.SubjectKey then do;40    FIRSTDTC=''; LASTDTC='';41  end;42    if ItemOID='IT.EX.FIRSTDTC' then FIRSTDTC=Value;43  if ItemOID='IT.EX.LASTDTC' then LASTDTC=Value;44  if last.SubjectKey then output;45run;46proc sql; create table joined as select a.*,b.FIRSTDTC,b.LASTDTC,c.RFICDTC,c.RFSTDTC,c.RFPENDTC from elements a left join dosing b on a.StudyOID=b.StudyOID and a.SubjectKey=b.SubjectKey inner join dm c on a.StudyOID=c.STUDYID and a.SubjectKey=c.USUBJID where not missing(a.ELEMENT); quit;47data result; set joined; length DOMAIN $2 STUDYID USUBJID ETCD SESTDTC SEENDTC SEUPDES $1024; DOMAIN='SE'; STUDYID=StudyOID; USUBJID=SubjectKey; ETCD=StudyEventOID; TAETORD=input(ORD,best32.); SESEQ=TAETORD; SEUPDES=''; SESTDY=.; SEENDY=.;48if EPOCH='SCREENING' then do; SESTDTC=RFICDTC; SEENDTC=FIRSTDTC; end; else if EPOCH='TREATMENT' then do; SESTDTC=FIRSTDTC; SEENDTC=LASTDTC; end; else do; SESTDTC=LASTDTC; SEENDTC=RFPENDTC; end;49if not missing(RFSTDTC) then do; if not missing(SESTDTC) then do; SESTDY=input(SESTDTC,yymmdd10.)-input(RFSTDTC,yymmdd10.); if SESTDY>=0 then SESTDY+1; end; if not missing(SEENDTC) then do; SEENDY=input(SEENDTC,yymmdd10.)-input(RFSTDTC,yymmdd10.); if SEENDY>=0 then SEENDY+1; end; end; run;50proc sql;51  create table final as select DOMAIN, STUDYID, USUBJID, SESEQ, ETCD, ELEMENT, TAETORD, EPOCH, SESTDTC, SEENDTC, SESTDY, SEENDY, SEUPDES from result;52quit;53proc export data=final outfile="/app/output/se.csv" dbms=csv replace; run;