Partial Adverse Event Dates

1library(yamaa)23ae <- yamaa_domain("spec.yaml")$output4ae

1import yamaa23ae = yamaa.yamaa_domain("spec.yaml").output4ae

1# Reference solution for the yamaa benchmark sdtm-ae-partial-dates (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)10library(stringr)1112odm <- read_csv(13  "/app/input/odm.csv",14  col_types = cols(.default = col_character())15)16dm <- read_csv(17  "/app/input/dm.csv",18  col_types = cols(.default = col_character())19)2021compose_dtc <- function(yr, mo, dy) {22  ifelse(23    is.na(yr) | yr == "", NA_character_,24    ifelse(25      is.na(mo) | mo == "", yr,26      ifelse(27        is.na(dy) | dy == "", paste0(yr, "-", str_pad(mo, 2, pad = "0")),28        paste0(yr, "-", str_pad(mo, 2, pad = "0"), "-", str_pad(dy, 2, pad = "0"))29      )30    )31  )32}3334study_day <- function(adt, ref) {35  diff <- as.integer(as.Date(adt) - as.Date(ref))36  ifelse(is.na(diff), NA_integer_, ifelse(diff >= 0L, diff + 1L, diff))37}3839# One record per form repeat; the repeat number is the sequence number.40# Dates stay at the precision collected: nothing is imputed.41ae <- odm |>42  filter(ItemGroupOID == "IG.AE") |>43  pivot_wider(44    id_cols = c(StudyOID, SubjectKey, FormRepeatKey),45    names_from = ItemOID,46    values_from = Value,47    values_fn = first48  ) |>49  mutate(50    AESEQ = as.integer(FormRepeatKey),51    AETERM = `IT.AE.AETERM`,52    AESTDTC = compose_dtc(`IT.AE.AESTYR`, `IT.AE.AESTMO`, `IT.AE.AESTDY`),53    AEENDTC = compose_dtc(`IT.AE.AEENYR`, `IT.AE.AEENMO`, `IT.AE.AEENDY`),54    START_FULL = !is.na(`IT.AE.AESTYR`) & `IT.AE.AESTYR` != "" &55      !is.na(`IT.AE.AESTMO`) & `IT.AE.AESTMO` != "" &56      !is.na(`IT.AE.AESTDY`) & `IT.AE.AESTDY` != "",57    END_FULL = !is.na(`IT.AE.AEENYR`) & `IT.AE.AEENYR` != "" &58      !is.na(`IT.AE.AEENMO`) & `IT.AE.AEENMO` != "" &59      !is.na(`IT.AE.AEENDY`) & `IT.AE.AEENDY` != ""60  ) |>61  left_join(62    dm |> select(USUBJID, RFSTDTC),63    by = c("SubjectKey" = "USUBJID")64  ) |>65  # Only a complete date gets a study day, and only when the reference66  # start date is known. Day 1 is the reference date; there is no day 0.67  mutate(68    AESTDY = if_else(69      START_FULL & !is.na(RFSTDTC) & RFSTDTC != "",70      study_day(AESTDTC, RFSTDTC), NA_integer_71    ),72    AEENDY = if_else(73      END_FULL & !is.na(RFSTDTC) & RFSTDTC != "",74      study_day(AEENDTC, RFSTDTC), NA_integer_75    ),76    DOMAIN = "AE",77    STUDYID = StudyOID,78    USUBJID = SubjectKey79  ) |>80  arrange(USUBJID, AESEQ) |>81  select(82    DOMAIN, STUDYID, USUBJID, AESEQ, AETERM,83    AESTDTC, AEENDTC, AESTDY, AEENDY84  )8586dir.create("/app/output", showWarnings = FALSE)87write_csv(ae, "/app/output/ae.csv", na = "")

1# Reference solution for the yamaa benchmark sdtm-ae-partial-dates (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 datetime import date8from pathlib import Path910import polars as pl111213def compose(yr: str | None, mo: str | None, dy: str | None) -> str | None:14    if yr is None or yr == "":15        return None16    if mo is None or mo == "":17        return yr18    mo = mo.zfill(2)19    if dy is None or dy == "":20        return f"{yr}-{mo}"21    return f"{yr}-{mo}-{dy.zfill(2)}"222324def complete(yr: str | None, mo: str | None, dy: str | None) -> bool:25    return bool(yr) and bool(mo) and bool(dy)262728def study_day(adt: date | None, ref: date | None) -> int | None:29    if adt is None or ref is None:30        return None31    delta = (adt - ref).days32    return delta + 1 if delta >= 0 else delta333435odm = pl.read_csv("/app/input/odm.csv", infer_schema=False)36dm = pl.read_csv("/app/input/dm.csv", infer_schema=False)3738# One record per form repeat; the repeat number is the sequence number.39# Dates stay at the precision collected: nothing is imputed.40wide = (41    odm.filter(pl.col("ItemGroupOID") == "IG.AE")42    .pivot(43        index=["StudyOID", "SubjectKey", "FormRepeatKey"],44        on="ItemOID",45        values="Value",46        aggregate_function="first",47    )48    .with_columns(AESEQ=pl.col("FormRepeatKey").cast(pl.Int64))49)5051ref = {52    row["USUBJID"]: (row["RFSTDTC"] or None) for row in dm.to_dicts()53}5455rows = []56for record in wide.to_dicts():57    usubjid = record["SubjectKey"]58    stdtc = compose(59        record.get("IT.AE.AESTYR"), record.get("IT.AE.AESTMO"), record.get("IT.AE.AESTDY")60    )61    endtc = compose(62        record.get("IT.AE.AEENYR"), record.get("IT.AE.AEENMO"), record.get("IT.AE.AEENDY")63    )64    # Only a complete date gets a study day, and only when the reference65    # start date is known. Day 1 is the reference date; there is no day 0.66    rf_raw = ref.get(usubjid)67    try:68        rf = date.fromisoformat(rf_raw) if rf_raw else None69    except ValueError:70        rf = None71    if complete(72        record.get("IT.AE.AESTYR"), record.get("IT.AE.AESTMO"), record.get("IT.AE.AESTDY")73    ):74        try:75            adt = date.fromisoformat(stdtc) if stdtc else None76        except ValueError:77            adt = None78        stdy = study_day(adt, rf)79    else:80        stdy = None81    if complete(82        record.get("IT.AE.AEENYR"), record.get("IT.AE.AEENMO"), record.get("IT.AE.AEENDY")83    ):84        try:85            adt = date.fromisoformat(endtc) if endtc else None86        except ValueError:87            adt = None88        endy = study_day(adt, rf)89    else:90        endy = None91    rows.append(92        {93            "DOMAIN": "AE",94            "STUDYID": record["StudyOID"],95            "USUBJID": usubjid,96            "AESEQ": record["AESEQ"],97            "AETERM": record.get("IT.AE.AETERM"),98            "AESTDTC": stdtc,99            "AEENDTC": endtc,100            "AESTDY": stdy,101            "AEENDY": endy,102        }103    )104105ae = pl.DataFrame(106    rows,107    schema={108        "DOMAIN": pl.String,109        "STUDYID": pl.String,110        "USUBJID": pl.String,111        "AESEQ": pl.Int64,112        "AETERM": pl.String,113        "AESTDTC": pl.String,114        "AEENDTC": pl.String,115        "AESTDY": pl.Int64,116        "AEENDY": pl.Int64,117    },118).sort(["USUBJID", "AESEQ"])119120Path("/app/output").mkdir(exist_ok=True)121ae.write_csv("/app/output/ae.csv")

1/* opensas reference solution for the yamaa benchmark sdtm-ae-partial-dates.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data dm;6  length STUDYID USUBJID RFSTDTC $1024;7  infile "/app/input/dm.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. RFSTDTC : $char1024.;9run;1011data odm;12  length StudyOID MetaDataVersionOID SubjectKey StudyEventOID StudyEventRepeatKey FormOID FormRepeatKey ItemGroupOID ItemGroupRepeatKey ItemOID Value $1024;13  infile "/app/input/odm.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input StudyOID : $char1024. MetaDataVersionOID : $char1024. SubjectKey : $char1024. StudyEventOID : $char1024. StudyEventRepeatKey : $char1024. FormOID : $char1024. FormRepeatKey : $char1024. ItemGroupOID : $char1024. ItemGroupRepeatKey : $char1024. ItemOID : $char1024. Value : $char1024.;15run;1617proc sort data=odm out=ordered; by StudyOID SubjectKey FormRepeatKey; run;18data wide;19  length AETERM AESTYR AESTMO AEENYR AEENMO STARTDAY ENDDAY $1024;20  retain AETERM AESTYR AESTMO AEENYR AEENMO STARTDAY ENDDAY;21  set ordered;22  where ItemGroupOID='IG.AE';23  by StudyOID SubjectKey FormRepeatKey;24  if first.FormRepeatKey then do;25    AETERM=''; AESTYR=''; AESTMO=''; AEENYR=''; AEENMO=''; STARTDAY=''; ENDDAY='';26  end;27    if ItemOID='IT.AE.AETERM' then AETERM=Value;28  if ItemOID='IT.AE.AESTYR' then AESTYR=Value;29  if ItemOID='IT.AE.AESTMO' then AESTMO=Value;30  if ItemOID='IT.AE.AEENYR' then AEENYR=Value;31  if ItemOID='IT.AE.AEENMO' then AEENMO=Value;32  if ItemOID='IT.AE.AESTDY' then STARTDAY=Value;33  if ItemOID='IT.AE.AEENDY' then ENDDAY=Value;34  if last.FormRepeatKey then output;35run;36data dates; set wide; length DOMAIN $2 STUDYID USUBJID AESTDTC AEENDTC $1024;37DOMAIN='AE'; STUDYID=StudyOID; USUBJID=SubjectKey; AESEQ=input(FormRepeatKey,best32.);38AESTDTC=''; AEENDTC='';39if not missing(AESTYR) then do; AESTDTC=AESTYR; if not missing(AESTMO) then do; AESTDTC=catx('-',AESTDTC,AESTMO); if not missing(STARTDAY) then AESTDTC=catx('-',AESTDTC,STARTDAY); end; end;40if not missing(AEENYR) then do; AEENDTC=AEENYR; if not missing(AEENMO) then do; AEENDTC=catx('-',AEENDTC,AEENMO); if not missing(ENDDAY) then AEENDTC=catx('-',AEENDTC,ENDDAY); end; end; run;41proc sql; create table joined as select a.*,b.RFSTDTC from dates a left join dm b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID; quit;42data result; set joined; AESTDY=.; AEENDY=.; if lengthn(RFSTDTC)=10 then do;43if lengthn(AESTDTC)=10 then do; AESTDY=input(AESTDTC,yymmdd10.)-input(RFSTDTC,yymmdd10.); if AESTDY>=0 then AESTDY+1; end;44if lengthn(AEENDTC)=10 then do; AEENDY=input(AEENDTC,yymmdd10.)-input(RFSTDTC,yymmdd10.); if AEENDY>=0 then AEENDY+1; end; end; run;45proc sql;46  create table final as select DOMAIN, STUDYID, USUBJID, AESEQ, AETERM, AESTDTC, AEENDTC, AESTDY, AEENDY from result;47quit;48proc export data=final outfile="/app/output/ae.csv" dbms=csv replace; run;