Questionnaire Items

1library(yamaa)23qs <- yamaa_domain("spec.yaml")$output4qs

1import yamaa23qs = yamaa.yamaa_domain("spec.yaml").output4qs

1# Reference solution for the yamaa benchmark sdtm-qs-questionnaire-items (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)1011items <- read_csv(12  "/app/input/items.csv",13  col_types = cols(ItemOrder = col_integer(), .default = col_character())14)15visits <- read_csv(16  "/app/input/visits.csv",17  col_types = cols(VISITNUM = col_integer(), .default = col_character())18)19notdone <- read_csv(20  "/app/input/notdone.csv",21  col_types = cols(.default = col_character())22)23odm <- read_csv(24  "/app/input/odm.csv",25  col_types = cols(.default = col_character())26)2728labels <- c(29  "0" = "Not at all",30  "1" = "Several days",31  "2" = "More than half the days",32  "3" = "Nearly every day"33)3435scores <- odm |>36  filter(!is.na(Value) & Value != "") |>37  select(SubjectKey, StudyEventOID, ItemOID, Value)3839skipped <- notdone |>40  filter(!is.na(ItemOID) & ItemOID != "") |>41  select(SubjectKey, StudyEventOID, ItemOID, Reason)4243refused <- notdone |>44  filter(is.na(ItemOID) | ItemOID == "") |>45  select(SubjectKey, StudyEventOID, Reason)4647first_visit <- visits |>48  group_by(SubjectKey) |>49  summarise(first_num = min(VISITNUM), .groups = "drop")5051# Every item at each visit, with the collected score or a NOT DONE record.52item_rows <- visits |>53  left_join(first_visit, by = "SubjectKey") |>54  cross_join(items) |>55  left_join(56    scores,57    by = c("SubjectKey", "StudyEventOID", "ItemOID")58  ) |>59  left_join(60    skipped,61    by = c("SubjectKey", "StudyEventOID", "ItemOID")62  ) |>63  left_join(64    refused |> select(SubjectKey, StudyEventOID) |> mutate(is_refused = TRUE),65    by = c("SubjectKey", "StudyEventOID")66  ) |>67  # A refused questionnaire contributes only its QSALL record below.68  filter(is.na(is_refused)) |>69  mutate(70    DOMAIN = "QS",71    STUDYID = StudyOID,72    USUBJID = SubjectKey,73    QSTESTCD = QSTESTCD,74    QSTEST = QSTEST,75    QSCAT = "PHQ-9",76    answered = !is.na(Value) & Value != "",77    QSORRES = if_else(answered, unname(labels[Value]), NA_character_),78    QSSTRESC = if_else(answered, Value, NA_character_),79    QSSTRESN = suppressWarnings(as.numeric(QSSTRESC)),80    QSSTAT = if_else(answered, NA_character_, "NOT DONE"),81    QSREASND = if_else(answered, NA_character_, Reason),82    QSBLFL = if_else(VISITNUM == first_num, "Y", NA_character_),83    QSDRVFL = NA_character_,84    QSDTC = VisitDate85  ) |>86  select(87    DOMAIN, STUDYID, USUBJID, QSTESTCD, QSTEST, QSCAT, QSORRES, QSSTRESC,88    QSSTRESN, QSSTAT, QSREASND, QSBLFL, QSDRVFL, VISITNUM, QSDTC, Value89  )9091totals <- item_rows |>92  group_by(STUDYID, USUBJID, VISITNUM, QSDTC, QSBLFL) |>93  summarise(94    n_answered = sum(!is.na(Value)),95    total = sum(suppressWarnings(as.numeric(Value)), na.rm = TRUE),96    .groups = "drop"97  ) |>98  filter(n_answered == 9) |>99  mutate(100    DOMAIN = "QS",101    QSTESTCD = "PHQ9T",102    QSTEST = "Patient Health Questionnaire 9 item total score",103    QSCAT = "PHQ-9",104    QSORRES = NA_character_,105    QSSTRESC = as.character(total),106    QSSTRESN = total,107    QSSTAT = NA_character_,108    QSREASND = NA_character_,109    QSDRVFL = "Y"110  ) |>111  select(112    DOMAIN, STUDYID, USUBJID, QSTESTCD, QSTEST, QSCAT, QSORRES, QSSTRESC,113    QSSTRESN, QSSTAT, QSREASND, QSBLFL, QSDRVFL, VISITNUM, QSDTC114  )115116refused_rows <- visits |>117  inner_join(refused, by = c("SubjectKey", "StudyEventOID")) |>118  left_join(first_visit, by = "SubjectKey") |>119  mutate(120    DOMAIN = "QS",121    STUDYID = StudyOID,122    USUBJID = SubjectKey,123    QSTESTCD = "QSALL",124    QSTEST = "All Questionnaires",125    QSCAT = "PHQ-9",126    QSORRES = NA_character_,127    QSSTRESC = NA_character_,128    QSSTRESN = NA_real_,129    QSSTAT = "NOT DONE",130    QSREASND = Reason,131    QSBLFL = if_else(VISITNUM == first_num, "Y", NA_character_),132    QSDRVFL = NA_character_,133    QSDTC = VisitDate134  ) |>135  select(136    DOMAIN, STUDYID, USUBJID, QSTESTCD, QSTEST, QSCAT, QSORRES, QSSTRESC,137    QSSTRESN, QSSTAT, QSREASND, QSBLFL, QSDRVFL, VISITNUM, QSDTC138  )139140qs <- bind_rows(141  item_rows |>142    select(-Value) |>143    mutate(QSSTRESN = suppressWarnings(as.numeric(QSSTRESC))),144  totals,145  refused_rows146) |>147  arrange(USUBJID, VISITNUM, QSTESTCD) |>148  group_by(USUBJID) |>149  mutate(QSSEQ = row_number()) |>150  ungroup() |>151  arrange(USUBJID, QSSEQ) |>152  select(153    DOMAIN, STUDYID, USUBJID, QSSEQ, QSTESTCD, QSTEST, QSCAT, QSORRES,154    QSSTRESC, QSSTRESN, QSSTAT, QSREASND, QSBLFL, QSDRVFL, VISITNUM, QSDTC155  )156157dir.create("/app/output", showWarnings = FALSE)158write_csv(qs, "/app/output/qs.csv", na = "")

1# Reference solution for the yamaa benchmark sdtm-qs-questionnaire-items (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) != ""141516items = pl.read_csv("/app/input/items.csv", infer_schema=False)17visits = pl.read_csv("/app/input/visits.csv", infer_schema=False)18notdone = pl.read_csv("/app/input/notdone.csv", infer_schema=False)19odm = pl.read_csv("/app/input/odm.csv", infer_schema=False)2021item_by_oid = {r["ItemOID"]: r for r in items.to_dicts()}22scores: dict[tuple, str] = {}23for row in odm.to_dicts():24    key = (str(row["SubjectKey"]), str(row["StudyEventOID"]), str(row["ItemOID"]))25    if _present(row["Value"]):26        scores[key] = str(row["Value"]).strip()2728refused: dict[tuple, str] = {}29skipped: dict[tuple, str] = {}30for row in notdone.to_dicts():31    key = (str(row["SubjectKey"]), str(row["StudyEventOID"]))32    oid, reason = str(row["ItemOID"] or ""), str(row["Reason"] or "")33    if not _present(oid):34        refused[key] = reason35    else:36        skipped[(key[0], key[1], oid)] = reason3738labels = {39    "0": "Not at all",40    "1": "Several days",41    "2": "More than half the days",42    "3": "Nearly every day",43}44total_test = "Patient Health Questionnaire 9 item total score"4546visit_by_key = {47    (str(r["SubjectKey"]), str(r["StudyEventOID"])): r for r in visits.to_dicts()48}49first_visit = {}50for row in visits.to_dicts():51    subj = str(row["SubjectKey"])52    num = int(row["VISITNUM"])53    first_visit[subj] = min(first_visit.get(subj, num), num)5455rows = []56for (subj, event), visit in visit_by_key.items():57    studyid = str(visit["StudyOID"])58    visitnum = str(visit["VISITNUM"])59    vsdtc = str(visit["VisitDate"])60    blfl = "Y" if int(visitnum) == first_visit[subj] else None61    if (subj, event) in refused:62        rows.append(63            {64                "DOMAIN": "QS",65                "STUDYID": studyid,66                "USUBJID": subj,67                "QSTESTCD": "QSALL",68                "QSTEST": "All Questionnaires",69                "QSCAT": "PHQ-9",70                "QSORRES": None,71                "QSSTRESC": None,72                "QSSTRESN": None,73                "QSSTAT": "NOT DONE",74                "QSREASND": refused[(subj, event)],75                "QSBLFL": blfl,76                "QSDRVFL": None,77                "VISITNUM": visitnum,78                "QSDTC": vsdtc,79            }80        )81        continue82    answered = []83    for oid, item in item_by_oid.items():84        testcd = str(item["QSTESTCD"])85        test = str(item["QSTEST"])86        score = scores.get((subj, event, oid))87        if _present(score):88            answered.append(int(score))89            rows.append(90                {91                    "DOMAIN": "QS",92                    "STUDYID": studyid,93                    "USUBJID": subj,94                    "QSTESTCD": testcd,95                    "QSTEST": test,96                    "QSCAT": "PHQ-9",97                    "QSORRES": labels[score],98                    "QSSTRESC": score,99                    "QSSTRESN": score,100                    "QSSTAT": None,101                    "QSREASND": None,102                    "QSBLFL": blfl,103                    "QSDRVFL": None,104                    "VISITNUM": visitnum,105                    "QSDTC": vsdtc,106                }107            )108        else:109            reason = skipped.get((subj, event, oid))110            rows.append(111                {112                    "DOMAIN": "QS",113                    "STUDYID": studyid,114                    "USUBJID": subj,115                    "QSTESTCD": testcd,116                    "QSTEST": test,117                    "QSCAT": "PHQ-9",118                    "QSORRES": None,119                    "QSSTRESC": None,120                    "QSSTRESN": None,121                    "QSSTAT": "NOT DONE",122                    "QSREASND": reason,123                    "QSBLFL": blfl,124                    "QSDRVFL": None,125                    "VISITNUM": visitnum,126                    "QSDTC": vsdtc,127                }128            )129    # The total appears only for a visit where all nine items were answered.130    if len(answered) == 9:131        total = sum(answered)132        rows.append(133            {134                "DOMAIN": "QS",135                "STUDYID": studyid,136                "USUBJID": subj,137                "QSTESTCD": "PHQ9T",138                "QSTEST": total_test,139                "QSCAT": "PHQ-9",140                "QSORRES": None,141                "QSSTRESC": str(total),142                "QSSTRESN": str(total),143                "QSSTAT": None,144                "QSREASND": None,145                "QSBLFL": blfl,146                "QSDRVFL": "Y",147                "VISITNUM": visitnum,148                "QSDTC": vsdtc,149            }150        )151152rows.sort(key=lambda r: (r["USUBJID"], int(r["VISITNUM"]), r["QSTESTCD"]))153for by_subj in sorted({r["USUBJID"] for r in rows}):154    for seq, row in enumerate(155        [r for r in rows if r["USUBJID"] == by_subj], start=1156    ):157        row["QSSEQ"] = str(seq)158159qs = (160    pl.DataFrame(161        rows,162        schema={163            "DOMAIN": pl.String,164            "STUDYID": pl.String,165            "USUBJID": pl.String,166            "QSSEQ": pl.String,167            "QSTESTCD": pl.String,168            "QSTEST": pl.String,169            "QSCAT": pl.String,170            "QSORRES": pl.String,171            "QSSTRESC": pl.String,172            "QSSTRESN": pl.String,173            "QSSTAT": pl.String,174            "QSREASND": pl.String,175            "QSBLFL": pl.String,176            "QSDRVFL": pl.String,177            "VISITNUM": pl.String,178            "QSDTC": pl.String,179        },180    )181    .with_columns(182        pl.col("QSSEQ").cast(pl.Int64).alias("_seq"),183        pl.col("VISITNUM").cast(pl.Int64).alias("_visit"),184    )185    .sort(["USUBJID", "_visit", "QSTESTCD"])186    .select(187        "DOMAIN", "STUDYID", "USUBJID", "QSSEQ", "QSTESTCD", "QSTEST", "QSCAT",188        "QSORRES", "QSSTRESC", "QSSTRESN", "QSSTAT", "QSREASND", "QSBLFL",189        "QSDRVFL", "VISITNUM", "QSDTC",190    )191)192193Path("/app/output").mkdir(exist_ok=True)194qs.write_csv("/app/output/qs.csv")

1/* opensas reference solution for the yamaa benchmark sdtm-qs-questionnaire-items.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data items;6  length ItemOID ItemOrder QSTESTCD QSTEST $1024;7  infile "/app/input/items.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input ItemOID : $char1024. ItemOrder : $char1024. QSTESTCD : $char1024. QSTEST : $char1024.;9run;1011data notdone;12  length StudyOID SubjectKey StudyEventOID ItemOID Reason $1024;13  infile "/app/input/notdone.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input StudyOID : $char1024. SubjectKey : $char1024. StudyEventOID : $char1024. ItemOID : $char1024. Reason : $char1024.;15run;1617data odm;18  length StudyOID MetaDataVersionOID SubjectKey StudyEventOID StudyEventRepeatKey ItemGroupOID ItemGroupRepeatKey ItemOID Value $1024;19  infile "/app/input/odm.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;20  input StudyOID : $char1024. MetaDataVersionOID : $char1024. SubjectKey : $char1024. StudyEventOID : $char1024. StudyEventRepeatKey : $char1024. ItemGroupOID : $char1024. ItemGroupRepeatKey : $char1024. ItemOID : $char1024. Value : $char1024.;21run;2223data visits;24  length StudyOID SubjectKey StudyEventOID VisitDate $1024;25  infile "/app/input/visits.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;26  input StudyOID : $char1024. SubjectKey : $char1024. StudyEventOID : $char1024. VISITNUM VisitDate : $char1024.;27run;2829proc sql;30create table answered as select a.*,b.QSTESTCD,b.QSTEST,c.VISITNUM,c.VisitDate from odm a inner join items b on a.ItemOID=b.ItemOID inner join visits c on a.StudyOID=c.StudyOID and a.SubjectKey=c.SubjectKey and a.StudyEventOID=c.StudyEventOID;31create table skipped as select a.*,b.QSTESTCD,b.QSTEST,c.VISITNUM,c.VisitDate from notdone a inner join items b on a.ItemOID=b.ItemOID inner join visits c on a.StudyOID=c.StudyOID and a.SubjectKey=c.SubjectKey and a.StudyEventOID=c.StudyEventOID;32create table refused as select a.*,c.VISITNUM,c.VisitDate from notdone a inner join visits c on a.StudyOID=c.StudyOID and a.SubjectKey=c.SubjectKey and a.StudyEventOID=c.StudyEventOID where missing(a.ItemOID);33quit;34data answers; set answered; length QSORRES QSSTRESC QSSTAT QSREASND QSDRVFL $1024; QSSTRESN=input(Value,best32.); QSSTRESC=strip(put(QSSTRESN,best32.)); QSORRES=''; if QSSTRESN=0 then QSORRES='Not at all'; if QSSTRESN=1 then QSORRES='Several days'; if QSSTRESN=2 then QSORRES='More than half the days'; if QSSTRESN=3 then QSORRES='Nearly every day'; QSSTAT=''; QSREASND=''; QSDRVFL=''; run;35proc sql; create table totals as select StudyOID,SubjectKey,StudyEventOID,VISITNUM,VisitDate,sum(QSSTRESN) as QSSTRESN from answers where not missing(QSSTRESN) group by StudyOID,SubjectKey,StudyEventOID,VISITNUM,VisitDate having count(*)=9; quit;36data totalout; set totals; length QSTESTCD QSTEST QSORRES QSSTRESC QSSTAT QSREASND QSDRVFL $1024; QSTESTCD='PHQ9T'; QSTEST='Patient Health Questionnaire 9 item total score'; QSORRES=''; QSSTRESC=strip(put(QSSTRESN,best32.)); QSSTAT=''; QSREASND=''; QSDRVFL='Y'; run;37data skippedout; set skipped; length QSORRES QSSTRESC QSSTAT QSREASND QSDRVFL $1024; QSORRES=''; QSSTRESC=''; QSSTRESN=.; QSSTAT='NOT DONE'; QSREASND=Reason; QSDRVFL=''; run;38data refusedout; set refused; length QSTESTCD QSTEST QSORRES QSSTRESC QSSTAT QSREASND QSDRVFL $1024; QSTESTCD='QSALL'; QSTEST='All Questionnaires'; QSORRES=''; QSSTRESC=''; QSSTRESN=.; QSSTAT='NOT DONE'; QSREASND=Reason; QSDRVFL=''; run;39data prepared; set answers totalout skippedout refusedout; length DOMAIN $2 STUDYID USUBJID QSCAT QSBLFL QSDTC $1024; DOMAIN='QS'; STUDYID=StudyOID; USUBJID=SubjectKey; QSCAT='PHQ-9'; QSDTC=VisitDate; QSBLFL=''; if VISITNUM=1 then QSBLFL='Y'; run;40proc sort data=prepared; by STUDYID USUBJID VISITNUM QSTESTCD; run;41data result; set prepared; by STUDYID USUBJID; retain QSSEQ;42  if first.USUBJID then QSSEQ=0;43  QSSEQ+1;44run;4546proc sql;47  create table final as select DOMAIN, STUDYID, USUBJID, QSSEQ, QSTESTCD, QSTEST, QSCAT, QSORRES, QSSTRESC, QSSTRESN, QSSTAT, QSREASND, QSBLFL, QSDRVFL, VISITNUM, QSDTC from result;48quit;49proc export data=final outfile="/app/output/qs.csv" dbms=csv replace; run;