Collected Vital Signs Form

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

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

1# Reference solution for the yamaa benchmark sdtm-vs-collected-form (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(purrr)9library(readr)10library(tidyr)1112fmt_text <- function(x) {13  if (is.na(x)) {14    return(NA_character_)15  }16  if (x == floor(x)) {17    formatC(x, format = "f", digits = 0)18  } else {19    format(x, scientific = FALSE, trim = TRUE, digits = 15)20  }21}2223odm <- read_csv(24  "/app/input/odm.csv",25  col_types = cols(.default = col_character())26)27tests <- read_csv(28  "/app/input/vs_tests.csv",29  col_types = cols(TESTORD = col_integer(), .default = col_character())30)3132wide <- odm |>33  select(StudyOID, SubjectKey, StudyEventOID, ItemOID, Value) |>34  pivot_wider(names_from = ItemOID, values_from = Value, values_fn = first)3536rows <- list()37for (i in seq_len(nrow(wide))) {38  visit <- wide[i, ]39  vsdtc <- visit$IT.VS.VSDTC40  position <- visit$IT.VS.POSITION41  location <- visit$IT.VS.TEMPLOC42  not_done <- !is.na(visit$IT.VS.BPNOTDONE) && visit$IT.VS.BPNOTDONE == "Y"43  reason <- visit$IT.VS.BPREASND44  for (j in seq_len(nrow(tests))) {45    test <- tests[j, ]46    testcd <- test$VSTESTCD47    result_item <- paste0("IT.VS.", testcd)48    unit_item <- paste0("IT.VS.", testcd, "U")49    result <- if (result_item %in% names(visit)) visit[[result_item]] else NA_character_50    unit <- if (unit_item %in% names(visit)) visit[[unit_item]] else NA_character_51    has_result <- !is.na(result) && result != ""52    if (testcd %in% c("SYSBP", "DIABP") && not_done) {53      has_result <- FALSE54    }55    if (!has_result) {56      orres <- NA_character_57      orresu <- NA_character_58      stresn <- NA_real_59      stresc <- NA_character_60      stresu <- NA_character_61      pos <- NA_character_62      loc <- NA_character_63    } else {64      orres <- result65      orresu <- unit66      stresn <- suppressWarnings(as.numeric(result))67      stresc <- fmt_text(stresn)68      stresu <- unit69      pos <- if (test$HAS_POSITION == "1") position else NA_character_70      loc <- if (test$HAS_LOCATION == "1") location else NA_character_71    }72    if (test$HAS_NOTDONE == "1" && not_done) {73      stat <- "NOT DONE"74      reasnd <- reason75    } else {76      stat <- NA_character_77      reasnd <- NA_character_78    }79    rows[[length(rows) + 1]] <- tibble(80      STUDYID = visit$StudyOID,81      USUBJID = visit$SubjectKey,82      VISIT = visit$StudyEventOID,83      VSTESTCD = testcd,84      VSTEST = test$VSTEST,85      TESTORD = test$TESTORD,86      VSORRES = orres,87      VSORRESU = orresu,88      VSSTRESN = stresn,89      VSSTRESC = stresc,90      VSSTRESU = stresu,91      VSPOS = pos,92      VSSTAT = stat,93      VSREASND = reasnd,94      VSLOC = loc,95      VSDTC = vsdtc96    )97  }98}99100vs <- bind_rows(rows) |>101  arrange(USUBJID, VSDTC, TESTORD) |>102  group_by(USUBJID) |>103  mutate(VSSEQ = row_number()) |>104  ungroup() |>105  arrange(USUBJID, VSSEQ) |>106  transmute(107    DOMAIN = "VS",108    STUDYID, USUBJID, VSSEQ, VISIT, VSTESTCD, VSTEST, VSORRES, VSORRESU,109    VSSTRESN, VSSTRESC, VSSTRESU, VSPOS, VSSTAT, VSREASND, VSLOC, VSDTC110  )111112dir.create("/app/output", showWarnings = FALSE)113write_csv(vs, "/app/output/vs.csv", na = "")

1# Reference solution for the yamaa benchmark sdtm-vs-collected-form (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 VS dataset from the collected vital signs form (ODM)8and the VS_TESTS test list.910One record per test per visit form. Reads /app/input, writes11/app/output/vs.csv.12"""1314import csv15import os16from collections import OrderedDict1718INPUT_DIR = "/app/input"19OUTPUT_DIR = "/app/output"2021COLUMNS = [22    "DOMAIN", "STUDYID", "USUBJID", "VSSEQ", "VISIT", "VSTESTCD",23    "VSTEST", "VSORRES", "VSORRESU", "VSSTRESN", "VSSTRESC", "VSSTRESU",24    "VSPOS", "VSSTAT", "VSREASND", "VSLOC", "VSDTC",25]2627BP_TESTS = {"SYSBP", "DIABP"}28POSITION_TESTS = {"SYSBP", "DIABP", "PULSE"}29LOCATION_TESTS = {"TEMP"}303132def num_text(value):33    """Write a collected numeric result as text: integers without a34    decimal point, other values in their plain decimal form."""35    number = float(value)36    if number == int(number):37        return str(int(number))38    return repr(number)394041def main():42    with open(os.path.join(INPUT_DIR, "vs_tests.csv"), newline="") as fh:43        tests = sorted(44            csv.DictReader(fh), key=lambda row: int(row["TESTORD"])45        )4647    with open(os.path.join(INPUT_DIR, "odm.csv"), newline="") as fh:48        odm_rows = list(csv.DictReader(fh))4950    # Group the form items by subject and visit form occurrence,51    # keeping first-seen order.52    forms = OrderedDict()53    for row in odm_rows:54        key = (55            row["StudyOID"],56            row["SubjectKey"],57            row["StudyEventOID"],58            row["StudyEventRepeatKey"],59            row["FormOID"],60            row["FormRepeatKey"],61            row["ItemGroupOID"],62            row["ItemGroupRepeatKey"],63        )64        form = forms.setdefault(key, {})65        item = row["ItemOID"].rsplit(".", 1)[-1]66        form[item] = row["Value"]6768    # Collect one entry per subject: list of (visit date, test records).69    subjects = OrderedDict()70    for (studyid, subjid, visit, *_rest), form in forms.items():71        vsdtc = form.get("VSDTC", "")72        position = form.get("POSITION", "")73        location = form.get("TEMPLOC", "")74        bp_not_done = form.get("BPNOTDONE", "") == "Y"75        bp_reason = form.get("BPREASND", "") if bp_not_done else ""7677        records = []78        for test in tests:79            code = test["VSTESTCD"]80            result = form.get(code, "")81            unit = form.get(code + "U", "") if result else ""82            if result:83                stresn = num_text(result)84                stresc = stresn85            else:86                stresn = ""87                stresc = ""88            records.append({89                "DOMAIN": "VS",90                "STUDYID": studyid,91                "USUBJID": subjid,92                "VISIT": visit,93                "VSTESTCD": code,94                "VSTEST": test["VSTEST"],95                "VSORRES": result,96                "VSORRESU": unit,97                "VSSTRESN": stresn,98                "VSSTRESC": stresc,99                "VSSTRESU": unit,100                "VSPOS": position101                if (code in POSITION_TESTS and result) else "",102                "VSSTAT": "NOT DONE"103                if (code in BP_TESTS and bp_not_done) else "",104                "VSREASND": bp_reason if code in BP_TESTS else "",105                "VSLOC": location106                if (code in LOCATION_TESTS and result) else "",107                "VSDTC": vsdtc,108            })109        subjects.setdefault(subjid, []).append((vsdtc, records))110111    out_rows = []112    for subjid, visits in subjects.items():113        visits.sort(key=lambda entry: entry[0])114        seq = 0115        for _vsdtc, records in visits:116            for record in records:117                seq += 1118                record["VSSEQ"] = seq119                out_rows.append(record)120121    os.makedirs(OUTPUT_DIR, exist_ok=True)122    with open(os.path.join(OUTPUT_DIR, "vs.csv"), "w", newline="") as fh:123        writer = csv.DictWriter(fh, fieldnames=COLUMNS)124        writer.writeheader()125        for record in out_rows:126            writer.writerow({col: record[col] for col in COLUMNS})127128129if __name__ == "__main__":130    main()

1/* opensas reference solution for the yamaa benchmark sdtm-vs-collected-form.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 FormOID FormRepeatKey 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. FormOID : $char1024. FormRepeatKey : $char1024. ItemGroupOID : $char1024. ItemGroupRepeatKey : $char1024. ItemOID : $char1024. Value : $char1024.;9run;1011data vs_tests;12  length VSTESTCD VSTEST TESTORD HAS_POSITION HAS_LOCATION HAS_NOTDONE $1024;13  infile "/app/input/vs_tests.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input VSTESTCD : $char1024. VSTEST : $char1024. TESTORD : $char1024. HAS_POSITION : $char1024. HAS_LOCATION : $char1024. HAS_NOTDONE : $char1024.;15run;1617proc sort data=odm out=ordered; by StudyOID SubjectKey StudyEventOID StudyEventRepeatKey FormOID FormRepeatKey; run;18data visits;19  length VSDTC POSITION TEMPLOC BPNOTDONE BPREASND $1024;20  retain VSDTC POSITION TEMPLOC BPNOTDONE BPREASND;21  set ordered;2223  by StudyOID SubjectKey StudyEventOID StudyEventRepeatKey FormOID FormRepeatKey;24  if first.FormRepeatKey then do;25    VSDTC=''; POSITION=''; TEMPLOC=''; BPNOTDONE=''; BPREASND='';26  end;27    if ItemOID='IT.VS.VSDTC' then VSDTC=Value;28  if ItemOID='IT.VS.POSITION' then POSITION=Value;29  if ItemOID='IT.VS.TEMPLOC' then TEMPLOC=Value;30  if ItemOID='IT.VS.BPNOTDONE' then BPNOTDONE=Value;31  if ItemOID='IT.VS.BPREASND' then BPREASND=Value;32  if last.FormRepeatKey then output;33run;34data tests; set vs_tests; length RESULTOID UNITOID $1024; RESULTOID=cats('IT.VS.',VSTESTCD); UNITOID=cats(RESULTOID,'U'); ORD=input(TESTORD,best32.); run;35proc sql; create table grid as select a.*,b.* from visits a cross join tests b;36create table joined as select a.*,b.Value as RESULTTEXT,c.Value as UNITTEXT from grid a left join odm b on a.StudyOID=b.StudyOID and a.SubjectKey=b.SubjectKey and a.StudyEventOID=b.StudyEventOID and a.StudyEventRepeatKey=b.StudyEventRepeatKey and a.FormOID=b.FormOID and a.FormRepeatKey=b.FormRepeatKey and a.RESULTOID=b.ItemOID left join odm c on a.StudyOID=c.StudyOID and a.SubjectKey=c.SubjectKey and a.StudyEventOID=c.StudyEventOID and a.StudyEventRepeatKey=c.StudyEventRepeatKey and a.FormOID=c.FormOID and a.FormRepeatKey=c.FormRepeatKey and a.UNITOID=c.ItemOID; quit;37data prepared; set joined; length DOMAIN $2 STUDYID USUBJID VISIT VSORRES VSORRESU VSSTRESC VSSTRESU VSPOS VSSTAT VSREASND VSLOC $1024;38DOMAIN='VS'; STUDYID=StudyOID; USUBJID=SubjectKey; VISIT=StudyEventOID; VSORRES=''; VSORRESU=''; VSSTRESN=.; VSSTRESC=''; VSSTRESU=''; VSPOS=''; VSSTAT=''; VSREASND=''; VSLOC='';39if HAS_NOTDONE='1' and BPNOTDONE='Y' then do; VSSTAT='NOT DONE'; VSREASND=BPREASND; end;40else if not missing(RESULTTEXT) then do; VSORRES=RESULTTEXT; VSORRESU=UNITTEXT; VSSTRESN=input(RESULTTEXT,best32.); VSSTRESC=strip(put(VSSTRESN,best15.)); VSSTRESU=UNITTEXT; if HAS_POSITION='1' then VSPOS=POSITION; if HAS_LOCATION='1' then VSLOC=TEMPLOC; end; run;41proc sort data=prepared; by STUDYID USUBJID VSDTC ORD; run;42data result; set prepared; by STUDYID USUBJID; retain VSSEQ;43  if first.USUBJID then VSSEQ=0;44  VSSEQ+1;45run;4647proc sql;48  create table final as select DOMAIN, STUDYID, USUBJID, VSSEQ, VISIT, VSTESTCD, VSTEST, VSORRES, VSORRESU, VSSTRESN, VSSTRESC, VSSTRESU, VSPOS, VSSTAT, VSREASND, VSLOC, VSDTC from result;49quit;50proc export data=final outfile="/app/output/vs.csv" dbms=csv replace; run;