Discontinuation Reasons

1library(yamaa)23ds <- yamaa_domain("spec.yaml")$output4ds

1import yamaa23ds = yamaa.yamaa_domain("spec.yaml").output4ds

1# Reference solution for the yamaa benchmark sdtm-ds-reasons (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)1011odm <- read_csv(12  "/app/input/odm.csv",13  col_types = cols(.default = col_character())14)1516wide <- odm |>17  filter(StudyEventOID %in% c("EOT", "EOS")) |>18  group_by(StudyOID, SubjectKey, StudyEventOID) |>19  summarise(20    DTC = Value[ItemOID == "IT.DS.DTC"][1],21    COMP = Value[ItemOID == "IT.DS.COMP"][1],22    REASON = Value[ItemOID == "IT.DS.REASON"][1],23    REASONCD = Value[ItemOID == "IT.DS.REASONCD"][1],24    .groups = "drop"25  )2627ds <- wide |>28  mutate(29    DOMAIN = "DS",30    STUDYID = StudyOID,31    USUBJID = SubjectKey,32    DSSEQ = ifelse(StudyEventOID == "EOT", 1L, 2L),33    DSCAT = "DISPOSITION EVENT",34    DSSCAT = ifelse(StudyEventOID == "EOT", "STUDY TREATMENT", "STUDY"),35    DSTERM = ifelse(COMP == "COMPLETED", "COMPLETED", na_if(REASON, "")),36    DSDECOD = ifelse(COMP == "COMPLETED", "COMPLETED", na_if(REASONCD, "")),37    DSSTDTC = suppressWarnings(as.Date(na_if(DTC, "")))38  ) |>39  select(DOMAIN, STUDYID, USUBJID, DSSEQ, DSCAT, DSSCAT, DSTERM, DSDECOD, DSSTDTC) |>40  arrange(USUBJID, DSSEQ)4142dir.create("/app/output", showWarnings = FALSE)43write_csv(ds, "/app/output/ds.csv", na = "")

1# Reference solution for the yamaa benchmark sdtm-ds-reasons (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 pl1011odm = pl.read_csv("/app/input/odm.csv", infer_schema=False)1213wide = (14    odm.group_by("StudyOID", "SubjectKey", "StudyEventOID")15    .agg(16        pl.col("Value").filter(pl.col("ItemOID") == "IT.DS.DTC").first().alias("DTC"),17        pl.col("Value").filter(pl.col("ItemOID") == "IT.DS.COMP").first().alias("COMP"),18        pl.col("Value").filter(pl.col("ItemOID") == "IT.DS.REASON").first().alias("REASON"),19        pl.col("Value")20        .filter(pl.col("ItemOID") == "IT.DS.REASONCD")21        .first()22        .alias("REASONCD"),23    )24    .filter(pl.col("StudyEventOID").is_in(["EOT", "EOS"]))25)2627MILESTONE = {"EOT": ("STUDY TREATMENT", 1), "EOS": ("STUDY", 2)}2829records: list[dict] = []30for row in wide.to_dicts():31    study = row["StudyOID"]32    subj = row["SubjectKey"]33    event = row["StudyEventOID"]34    sscat, seq = MILESTONE[event]35    comp = row["COMP"] or ""36    reason = row["REASON"] or ""37    reasoncd = row["REASONCD"] or ""38    dtc = row["DTC"] or ""39    if comp == "COMPLETED":40        term, decod = "COMPLETED", "COMPLETED"41    else:42        term, decod = (reason or None), (reasoncd or None)43    usubjid = subj44    records.append(45        {46            "DOMAIN": "DS",47            "STUDYID": study,48            "USUBJID": usubjid,49            "DSSEQ": seq,50            "DSCAT": "DISPOSITION EVENT",51            "DSSCAT": sscat,52            "DSTERM": term,53            "DSDECOD": decod,54            "DSSTDTC": dtc or None,55        }56    )5758ds = pl.DataFrame(59    records,60    schema={61        "DOMAIN": pl.String,62        "STUDYID": pl.String,63        "USUBJID": pl.String,64        "DSSEQ": pl.Int64,65        "DSCAT": pl.String,66        "DSSCAT": pl.String,67        "DSTERM": pl.String,68        "DSDECOD": pl.String,69        "DSSTDTC": pl.String,70    },71).sort(["USUBJID", "DSSEQ"])7273Path("/app/output").mkdir(exist_ok=True)74ds.write_csv("/app/output/ds.csv")

1/* opensas reference solution for the yamaa benchmark sdtm-ds-reasons.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 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. ItemGroupOID : $char1024. ItemGroupRepeatKey : $char1024. ItemOID : $char1024. Value : $char1024.;9run;1011proc sort data=odm out=ordered; by StudyOID SubjectKey StudyEventOID; run;12data wide;13  length COMP DTC REASON REASONCD $1024;14  retain COMP DTC REASON REASONCD;15  set ordered;1617  by StudyOID SubjectKey StudyEventOID;18  if first.StudyEventOID then do;19    COMP=''; DTC=''; REASON=''; REASONCD='';20  end;21    if ItemOID='IT.DS.COMP' then COMP=Value;22  if ItemOID='IT.DS.DTC' then DTC=Value;23  if ItemOID='IT.DS.REASON' then REASON=Value;24  if ItemOID='IT.DS.REASONCD' then REASONCD=Value;25  if last.StudyEventOID then output;26run;27data prepared; set wide; length DOMAIN $2 STUDYID USUBJID DSTERM DSDECOD DSCAT DSSCAT DSSTDTC $1024;28DOMAIN='DS'; STUDYID=StudyOID; USUBJID=SubjectKey; DSCAT='DISPOSITION EVENT'; DSSTDTC=DTC; DSTERM=REASON; DSDECOD=REASONCD;29if COMP='COMPLETED' then do; DSTERM='COMPLETED'; DSDECOD='COMPLETED'; end;30if StudyEventOID='EOT' then do; DSSEQ=1; DSSCAT='STUDY TREATMENT'; end; else do; DSSEQ=2; DSSCAT='STUDY'; end; run; data result; set prepared; run;31proc sql;32  create table final as select DOMAIN, STUDYID, USUBJID, DSSEQ, DSCAT, DSSCAT, DSTERM, DSDECOD, DSSTDTC from result;33quit;34proc export data=final outfile="/app/output/ds.csv" dbms=csv replace; run;