Collected Vital Signs Form

1library(yamaa)23vs <- yamaa_domain("spec.yaml")$output4vs

1import yamaa23vs = yamaa.yamaa_domain("spec.yaml").output4vs

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  method <- visit$IT.VS.TEMPMETHOD42  not_done <- !is.na(visit$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$VSTESTCD47    result_item <- paste0("IT.VS.", testcd)48    unit_item <- paste0("IT.VS.", testcd, "U")49    result <- if (result_item %in% names(visit)) visit[[result_item]] else NA_character_50    unit <- if (unit_item %in% names(visit)) visit[[unit_item]] else NA_character_51    has_result <- !is.na(result) && result != ""52    if (testcd %in% c("SYSBP", "DIABP") && not_done) {53      has_result <- FALSE54    }55    if (!has_result) {56      orres <- NA_character_57      orresu <- NA_character_58      stresn <- NA_real_59      stresc <- NA_character_60      stresu <- NA_character_61      pos <- NA_character_62      meth <- NA_character_63    } else {64      orres <- result65      orresu <- unit66      stresn <- suppressWarnings(as.numeric(result))67      stresc <- fmt_text(stresn)68      stresu <- unit69      pos <- if (test$HAS_POSITION == "1") position else NA_character_70      meth <- if (test$HAS_METHOD == "1") method else NA_character_71    }72    if (test$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      VSMETHOD = meth,93      VSSTAT = stat,94      VSREASND = reasnd,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, VSMETHOD, VSSTAT, VSREASND, 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 1.67from pathlib import Path89import polars as pl101112def fmt_text(x: float | None) -> str | None:13    if x is None:14        return None15    import math1617    if isinstance(x, float) and (math.isnan(x) or math.isinf(x)):18        return None19    if float(x).is_integer():20        return str(int(float(x)))21    return f"{float(x):.15g}"222324odm = pl.read_csv("/app/input/odm.csv", infer_schema=False)25tests = pl.read_csv("/app/input/vs_tests.csv", infer_schema=False).with_columns(26    pl.col("TESTORD").cast(pl.Int64),27)2829test_list = sorted(tests.to_dicts(), key=lambda r: r["TESTORD"])3031# One wide form per subject per visit: its date, position, method, not-done32# flag, reason, and each test's result and unit.33visits: dict[tuple[str, str], dict] = {}34for row in odm.to_dicts():35    key = (row["SubjectKey"], row["StudyEventOID"])36    entry = visits.setdefault(37        key,38        {39            "study": row["StudyOID"],40            "subject": row["SubjectKey"],41            "visit": row["StudyEventOID"],42            "items": {},43        },44    )45    entry["items"][row["ItemOID"]] = row["Value"]4647records = []48for entry in visits.values():49    items = entry["items"]50    vsdtc = items.get("IT.VS.VSDTC")51    position = items.get("IT.VS.POSITION")52    method = items.get("IT.VS.TEMPMETHOD")53    not_done = items.get("IT.VS.BPNOTDONE") == "Y"54    reason = items.get("IT.VS.BPREASND")55    for test in test_list:56        testcd = test["VSTESTCD"]57        result_item = f"IT.VS.{testcd}"58        unit_item = f"IT.VS.{testcd}U"59        # WEIGHT unit in the form is IT.VS.WEIGHTU, which fits the pattern;60        # the same holds for every test.61        result = items.get(result_item)62        unit = items.get(unit_item)63        has_result = result is not None and result != ""64        if testcd in ("SYSBP", "DIABP") and not_done:65            has_result = False66            result = None67            unit = None68        if not has_result:69            orres = None70            orresu = None71            stresn = None72            stresc = None73            stresu = None74            pos = None75            meth = None76        else:77            orres = result78            orresu = unit79            stresn = float(result)80            stresc = fmt_text(stresn)81            stresu = unit82            pos = position if test["HAS_POSITION"] == "1" else None83            meth = method if test["HAS_METHOD"] == "1" else None84        if test["HAS_NOTDONE"] == "1" and not_done:85            stat = "NOT DONE"86            reasnd = reason87        else:88            stat = None89            reasnd = None90        records.append(91            {92                "DOMAIN": "VS",93                "STUDYID": entry["study"],94                "USUBJID": entry["subject"],95                "VISIT": entry["visit"],96                "VSTESTCD": testcd,97                "VSTEST": test["VSTEST"],98                "_testord": test["TESTORD"],99                "VSORRES": orres,100                "VSORRESU": orresu,101                "VSSTRESN": stresn,102                "VSSTRESC": stresc,103                "VSSTRESU": stresu,104                "VSPOS": pos,105                "VSMETHOD": meth,106                "VSSTAT": stat,107                "VSREASND": reasnd,108                "VSDTC": vsdtc,109                "_vsdtc": vsdtc or "",110            }111        )112113vs = (114    pl.DataFrame(records)115    .sort(["USUBJID", "_vsdtc", "_testord"])116    .with_columns(VSSEQ=pl.int_range(1, pl.len() + 1).over("USUBJID"))117    .sort(["USUBJID", "VSSEQ"])118    .select(119        "DOMAIN",120        "STUDYID",121        "USUBJID",122        "VSSEQ",123        "VISIT",124        "VSTESTCD",125        "VSTEST",126        "VSORRES",127        "VSORRESU",128        "VSSTRESN",129        "VSSTRESC",130        "VSSTRESU",131        "VSPOS",132        "VSMETHOD",133        "VSSTAT",134        "VSREASND",135        "VSDTC",136    )137)138139Path("/app/output").mkdir(exist_ok=True)140vs.write_csv("/app/output/vs.csv")

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_METHOD 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_METHOD : $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 TEMPMETHOD BPNOTDONE BPREASND $1024;20  retain VSDTC POSITION TEMPMETHOD BPNOTDONE BPREASND;21  set ordered;2223  by StudyOID SubjectKey StudyEventOID StudyEventRepeatKey FormOID FormRepeatKey;24  if first.FormRepeatKey then do;25    VSDTC=''; POSITION=''; TEMPMETHOD=''; 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.TEMPMETHOD' then TEMPMETHOD=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 VSMETHOD VSSTAT VSREASND $1024;38DOMAIN='VS'; STUDYID=StudyOID; USUBJID=SubjectKey; VISIT=StudyEventOID; VSORRES=''; VSORRESU=''; VSSTRESN=.; VSSTRESC=''; VSSTRESU=''; VSPOS=''; VSMETHOD=''; VSSTAT=''; VSREASND='';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_METHOD='1' then VSMETHOD=TEMPMETHOD; 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, VSMETHOD, VSSTAT, VSREASND, VSDTC from result;49quit;50proc export data=final outfile="/app/output/vs.csv" dbms=csv replace; run;