Prior Procedures from Surgery and Radiotherapy Forms

1library(yamaa)23pr <- yamaa_domain("spec.yaml")$output4pr

1import yamaa23pr = yamaa.yamaa_domain("spec.yaml").output4pr

1# Reference solution for the yamaa benchmark sdtm-pr-procedures (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)1011odm <- read_csv(12  "/app/input/odm.csv",13  col_types = cols(.default = col_character())14)1516wide <- odm |>17  mutate(Value = na_if(Value, "")) |>18  pivot_wider(19    id_cols = c(StudyOID, SubjectKey, StudyEventOID, ItemGroupOID, ItemGroupRepeatKey),20    names_from = ItemOID,21    values_from = Value,22    values_fn = function(x) x[[1]]23  )2425pr <- wide |>26  mutate(27    STUDYID = StudyOID,28    # USUBJID carries the study prefix when the ODM subject key does not.29    USUBJID = if_else(30      startsWith(SubjectKey, paste0(StudyOID, "-")),31      SubjectKey, paste0(StudyOID, "-", SubjectKey)32    ),33    DOMAIN = "PR",34    PRTRT = IT.PR.PRTRT,35    PRCAT = case_when(36      ItemGroupOID == "IG.PR.SURGERY" ~ "PRIOR CANCER SURGERY",37      ItemGroupOID == "IG.PR.RADIOTHERAPY" ~ "PRIOR RADIOTHERAPY"38    ),39    PRPRESP = if_else(ItemGroupOID == "IG.PR.RADIOTHERAPY", "Y", NA_character_),40    PROCCUR = if_else(41      ItemGroupOID == "IG.PR.RADIOTHERAPY", IT.PR.RTPRSP, NA_character_42    ),43    PRLOC = if_else(ItemGroupOID == "IG.PR.SURGERY", IT.PR.PRLOC, NA_character_),44    PRLAT = if_else(ItemGroupOID == "IG.PR.SURGERY", IT.PR.PRLAT, NA_character_),45    PRDOSE = if_else(46      ItemGroupOID == "IG.PR.RADIOTHERAPY" & PROCCUR == "Y",47      IT.PR.PRDOSE, NA_character_48    ),49    PRDOSU = if_else(50      ItemGroupOID == "IG.PR.RADIOTHERAPY" & PROCCUR == "Y",51      IT.PR.PRDOSU, NA_character_52    ),53    PRSTDTC = case_when(54      ItemGroupOID == "IG.PR.RADIOTHERAPY" & PROCCUR == "Y" ~ IT.PR.PRSTDTC,55      ItemGroupOID == "IG.PR.SURGERY" ~ IT.PR.PRSTDTC,56      TRUE ~ NA_character_57    ),58    PRENDTC = if_else(59      ItemGroupOID == "IG.PR.RADIOTHERAPY" & PROCCUR == "Y",60      IT.PR.PRENDTC, NA_character_61    )62  ) |>63  arrange(USUBJID, is.na(PRSTDTC), PRSTDTC, PRTRT) |>64  group_by(USUBJID) |>65  mutate(PRSEQ = row_number()) |>66  ungroup() |>67  arrange(USUBJID, PRSEQ) |>68  select(69    DOMAIN, STUDYID, USUBJID, PRSEQ, PRTRT, PRCAT, PRPRESP, PROCCUR,70    PRLOC, PRLAT, PRDOSE, PRDOSU, PRSTDTC, PRENDTC71  )7273dir.create("/app/output", showWarnings = FALSE)74write_csv(pr, "/app/output/pr.csv", na = "")

1# Reference solution for the yamaa benchmark sdtm-pr-procedures (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 pl101112def _present(value) -> bool:13    return value is not None and str(value) != ""141516odm = pl.read_csv("/app/input/odm.csv", infer_schema=False)1718# One record per reported procedure and per answer to the pre-specified19# radiotherapy question: each form occurrence is a record.20groups: dict[tuple, dict] = {}21for row in odm.to_dicts():22    key = (23        str(row["StudyOID"]),24        str(row["SubjectKey"]),25        str(row["StudyEventOID"]),26        str(row["ItemGroupOID"]),27        str(row["ItemGroupRepeatKey"]),28    )29    groups.setdefault(key, {})[str(row["ItemOID"])] = row["Value"]3031cat_by_group = {32    "IG.PR.SURGERY": "PRIOR CANCER SURGERY",33    "IG.PR.RADIOTHERAPY": "PRIOR RADIOTHERAPY",34}3536rows = []37for (studyid, subjkey, _event, group_oid, _rep), values in groups.items():38    # USUBJID carries the study prefix when the ODM subject key does not.39    usubjid = subjkey if subjkey.startswith(studyid + "-") else f"{studyid}-{subjkey}"40    is_radio = group_oid == "IG.PR.RADIOTHERAPY"41    occurs = str(values.get("IT.PR.RTPRSP") or "") if is_radio else ""42    prtrt = str(values.get("IT.PR.PRTRT") or "")43    if is_radio:44        prpresp, procur = "Y", occurs if _present(occurs) else None45    else:46        prpresp, procur = None, None47    # Dose only when the procedure occurred; a "No" keeps no dose or dates.48    if is_radio and procur == "Y":49        dose = str(values.get("IT.PR.PRDOSE") or "")50        dose = dose if _present(dose) else None51        dosu = str(values.get("IT.PR.PRDOSU") or "")52        dosu = dosu if _present(dosu) else None53        stdtc = str(values.get("IT.PR.PRSTDTC") or "")54        stdtc = stdtc if _present(stdtc) else None55        endtc = str(values.get("IT.PR.PRENDTC") or "")56        endtc = endtc if _present(endtc) else None57    elif not is_radio:58        dose = dosu = None59        stdtc = str(values.get("IT.PR.PRSTDTC") or "")60        stdtc = stdtc if _present(stdtc) else None61        endtc = None62        # Surgery has no end date in the form.63        if "IT.PR.PRENDTC" in values and _present(values.get("IT.PR.PRENDTC")):64            endtc = str(values.get("IT.PR.PRENDTC"))65    else:66        dose = dosu = stdtc = endtc = None67    rows.append(68        {69            "DOMAIN": "PR",70            "STUDYID": studyid,71            "USUBJID": usubjid,72            "PRTRT": prtrt,73            "PRCAT": cat_by_group[group_oid],74            "PRPRESP": prpresp,75            "PROCCUR": procur,76            "PRLOC": str(values.get("IT.PR.PRLOC") or "") or None,77            "PRLAT": str(values.get("IT.PR.PRLAT") or "") or None,78            "PRDOSE": dose,79            "PRDOSU": dosu,80            "PRSTDTC": stdtc,81            "PRENDTC": endtc,82        }83    )8485# PRSEQ numbers each subject's records by start date, then procedure name.86rows.sort(key=lambda r: (r["USUBJID"], r["PRSTDTC"] is None, r["PRSTDTC"] or "", r["PRTRT"]))87seq_by_subject: dict[str, int] = {}88for row in rows:89    seq_by_subject[row["USUBJID"]] = seq_by_subject.get(row["USUBJID"], 0) + 190    row["PRSEQ"] = str(seq_by_subject[row["USUBJID"]])9192pr = (93    pl.DataFrame(94        rows,95        schema={96            "DOMAIN": pl.String,97            "STUDYID": pl.String,98            "USUBJID": pl.String,99            "PRSEQ": pl.String,100            "PRTRT": pl.String,101            "PRCAT": pl.String,102            "PRPRESP": pl.String,103            "PROCCUR": pl.String,104            "PRLOC": pl.String,105            "PRLAT": pl.String,106            "PRDOSE": pl.String,107            "PRDOSU": pl.String,108            "PRSTDTC": pl.String,109            "PRENDTC": pl.String,110        },111    )112    .with_columns(pl.col("PRSEQ").cast(pl.Int64).alias("_seq"))113    .sort(["USUBJID", "_seq"])114    .select(115        "DOMAIN", "STUDYID", "USUBJID", "PRSEQ", "PRTRT", "PRCAT", "PRPRESP",116        "PROCCUR", "PRLOC", "PRLAT", "PRDOSE", "PRDOSU", "PRSTDTC", "PRENDTC",117    )118)119120Path("/app/output").mkdir(exist_ok=True)121pr.write_csv("/app/output/pr.csv")

1/* opensas reference solution for the yamaa benchmark sdtm-pr-procedures.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 ItemGroupOID ItemGroupRepeatKey; run;12data wide;13  length PRTRT PRLOC PRLAT PRDOSU PRSTDTC PRENDTC RTPRSP DOSETEXT $1024;14  retain PRTRT PRLOC PRLAT PRDOSU PRSTDTC PRENDTC RTPRSP DOSETEXT;15  set ordered;1617  by StudyOID SubjectKey ItemGroupOID ItemGroupRepeatKey;18  if first.ItemGroupRepeatKey then do;19    PRTRT=''; PRLOC=''; PRLAT=''; PRDOSU=''; PRSTDTC=''; PRENDTC=''; RTPRSP=''; DOSETEXT='';20  end;21    if ItemOID='IT.PR.PRTRT' then PRTRT=Value;22  if ItemOID='IT.PR.PRLOC' then PRLOC=Value;23  if ItemOID='IT.PR.PRLAT' then PRLAT=Value;24  if ItemOID='IT.PR.PRDOSU' then PRDOSU=Value;25  if ItemOID='IT.PR.PRSTDTC' then PRSTDTC=Value;26  if ItemOID='IT.PR.PRENDTC' then PRENDTC=Value;27  if ItemOID='IT.PR.RTPRSP' then RTPRSP=Value;28  if ItemOID='IT.PR.PRDOSE' then DOSETEXT=Value;29  if last.ItemGroupRepeatKey then output;30run;31data prepared; set wide; length DOMAIN $2 STUDYID USUBJID PRCAT PRPRESP PROCCUR $1024;32DOMAIN='PR'; STUDYID=StudyOID; USUBJID=catx('-',StudyOID,SubjectKey); PRPRESP=''; PROCCUR=''; PRDOSE=.;33if ItemGroupOID='IG.PR.SURGERY' then do; PRCAT='PRIOR CANCER SURGERY'; PRENDTC=''; end;34else if ItemGroupOID='IG.PR.RADIOTHERAPY' then do; PRCAT='PRIOR RADIOTHERAPY'; PRPRESP='Y'; PROCCUR=RTPRSP; PRLOC=''; PRLAT=''; if RTPRSP='Y' then PRDOSE=input(DOSETEXT,best32.); else do; PRDOSU=''; PRSTDTC=''; PRENDTC=''; end; end; else delete; run;35proc sort data=prepared; by STUDYID USUBJID PRSTDTC PRTRT; run;36data result; set prepared; by STUDYID USUBJID; retain PRSEQ;37  if first.USUBJID then PRSEQ=0;38  PRSEQ+1;39run;4041proc sql;42  create table final as select DOMAIN, STUDYID, USUBJID, PRSEQ, PRTRT, PRCAT, PRPRESP, PROCCUR, PRLOC, PRLAT, PRDOSE, PRDOSU, PRSTDTC, PRENDTC from result;43quit;44proc export data=final outfile="/app/output/pr.csv" dbms=csv replace; run;