Questionnaire Items

1library(yamaa)23yamaa_spec("spec.yaml")$run()$output

1import yamaa23yamaa.spec("spec.yaml").run().output

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 1.67"""Build the SDTM QS dataset (PHQ-9) from ITEMS, NOTDONE, ODM and VISITS."""89import csv10import os1112INPUT_DIR = "/app/input"13OUTPUT_DIR = "/app/output"1415RESPONSE_TEXT = {16    0: "Not at all",17    1: "Several days",18    2: "More than half the days",19    3: "Nearly every day",20}2122COLUMNS = [23    "DOMAIN", "STUDYID", "USUBJID", "QSSEQ", "QSTESTCD", "QSTEST",24    "QSCAT", "QSORRES", "QSSTRESC", "QSSTRESN", "QSSTAT", "QSREASND",25    "QSBLFL", "QSDRVFL", "VISITNUM", "QSDTC",26]272829def read_csv(name):30    with open(os.path.join(INPUT_DIR, name), newline="", encoding="utf-8") as fh:31        return list(csv.DictReader(fh))323334def main():35    items = read_csv("items.csv")36    notdone = read_csv("notdone.csv")37    odm = read_csv("odm.csv")38    visits = read_csv("visits.csv")3940    # Item metadata keyed by ItemOID, kept in ITEMS order.41    item_by_oid = {row["ItemOID"]: row for row in items}4243    # Visit number and collection date per (subject, study event).44    visit_info = {}45    for row in visits:46        visit_info[(row["SubjectKey"], row["StudyEventOID"])] = (47            int(row["VISITNUM"]),48            row["VisitDate"],49        )5051    # Collected scores: (subject, event, item oid) -> int score.52    collected = {}53    study_by_subject = {}54    for row in odm:55        study_by_subject[row["SubjectKey"]] = row["StudyOID"]56        if row["ItemOID"] in item_by_oid:57            collected[(row["SubjectKey"], row["StudyEventOID"], row["ItemOID"])] = int(row["Value"])5859    # Not-done declarations: whole questionnaire (item oid empty) or per item.60    refused = {}       # (subject, event) -> reason61    skipped = {}       # (subject, event, item oid) -> reason62    for row in notdone:63        key = (row["SubjectKey"], row["StudyEventOID"])64        if row["ItemOID"]:65            skipped[key + (row["ItemOID"],)] = row["Reason"]66        else:67            refused[key] = row["Reason"]6869    # Every subject/visit seen in ODM, NOTDONE or VISITS.70    subject_events = set()71    for subject, event in visit_info:72        subject_events.add((subject, event))73    for subject, event, _oid in collected:74        subject_events.add((subject, event))75    for subject, event in refused:76        subject_events.add((subject, event))77    for subject, event, _oid in skipped:78        subject_events.add((subject, event))7980    def sort_key(se):81        subject, event = se82        visitnum = visit_info.get((subject, event), (0, ""))[0]83        return (subject, visitnum, event)8485    records = []86    for subject, event in sorted(subject_events, key=sort_key):87        visitnum, visit_date = visit_info.get((subject, event), ("", ""))88        studyid = study_by_subject.get(subject, "")89        blfl = "Y" if visitnum == 1 else ""90        base = {91            "DOMAIN": "QS",92            "STUDYID": studyid,93            "USUBJID": subject,94            "QSCAT": "PHQ-9",95            "VISITNUM": visitnum,96            "QSDTC": visit_date,97            "QSBLFL": blfl,98        }99        visit_records = []100        if (subject, event) in refused:101            rec = dict(base)102            rec.update({103                "QSTESTCD": "QSALL",104                "QSTEST": "All Questionnaires",105                "QSORRES": "",106                "QSSTRESC": "",107                "QSSTRESN": "",108                "QSSTAT": "NOT DONE",109                "QSREASND": refused[(subject, event)],110                "QSDRVFL": "",111            })112            visit_records.append(rec)113        else:114            answered = 0115            total = 0116            for item in items:117                oid = item["ItemOID"]118                key = (subject, event, oid)119                rec = dict(base)120                rec.update({121                    "QSTESTCD": item["QSTESTCD"],122                    "QSTEST": item["QSTEST"],123                    "QSDRVFL": "",124                })125                if key in skipped:126                    rec.update({127                        "QSORRES": "",128                        "QSSTRESC": "",129                        "QSSTRESN": "",130                        "QSSTAT": "NOT DONE",131                        "QSREASND": skipped[key],132                    })133                elif key in collected:134                    score = collected[key]135                    answered += 1136                    total += score137                    rec.update({138                        "QSORRES": RESPONSE_TEXT[score],139                        "QSSTRESC": str(score),140                        "QSSTRESN": score,141                        "QSSTAT": "",142                        "QSREASND": "",143                    })144                else:145                    continue146                visit_records.append(rec)147            if answered == len(items):148                rec = dict(base)149                rec.update({150                    "QSTESTCD": "PHQ9T",151                    "QSTEST": "Patient Health Questionnaire 9 item total score",152                    "QSORRES": "",153                    "QSSTRESC": str(total),154                    "QSSTRESN": total,155                    "QSSTAT": "",156                    "QSREASND": "",157                    "QSDRVFL": "Y",158                })159                visit_records.append(rec)160        # QSSEQ within the visit follows QSTESTCD order; the total-score161        # record (PHQ9T) and the refused record (QSALL) sort last anyway.162        visit_records.sort(key=lambda r: r["QSTESTCD"])163        records.extend(visit_records)164165    # QSSEQ numbers each subject's records from 1.166    seq_by_subject = {}167    for rec in records:168        subject = rec["USUBJID"]169        seq_by_subject[subject] = seq_by_subject.get(subject, 0) + 1170        rec["QSSEQ"] = seq_by_subject[subject]171172    os.makedirs(OUTPUT_DIR, exist_ok=True)173    with open(os.path.join(OUTPUT_DIR, "qs.csv"), "w", newline="", encoding="utf-8") as fh:174        writer = csv.DictWriter(fh, fieldnames=COLUMNS)175        writer.writeheader()176        for rec in records:177            writer.writerow({col: rec.get(col, "") for col in COLUMNS})178179180if __name__ == "__main__":181    main()

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;