Summarize End-of-Study and End-of-Treatment Disposition

1library(yamaa)23adsl <- yamaa_domain("spec.yaml")$output4adsl

1import yamaa23adsl = yamaa.yamaa_domain("spec.yaml").output4adsl

1# Reference solution for the yamaa benchmark adam-adsl-disposition (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)910dm <- read_csv(11  "/app/input/dm.csv",12  col_types = cols(.default = col_character())13)14ds <- read_csv(15  "/app/input/ds.csv",16  col_types = cols(DSSEQ = col_integer(), DSSTDTC = col_date(), .default = col_character())17)1819# The last dated disposition event per track: latest date, highest sequence20# on a tie. The study track reads every epoch but TREATMENT; the treatment21# track reads only TREATMENT.22last_study <- ds |>23  filter(DSCAT %in% "DISPOSITION EVENT", EPOCH != "TREATMENT", !is.na(DSSTDTC)) |>24  arrange(STUDYID, USUBJID, desc(DSSTDTC), desc(DSSEQ)) |>25  distinct(STUDYID, USUBJID, .keep_all = TRUE) |>26  transmute(STUDYID, USUBJID, EOSDT = DSSTDTC, EOSDECOD = DSDECOD, EOSREAS = DSTERM)2728last_trt <- ds |>29  filter(DSCAT %in% "DISPOSITION EVENT", EPOCH %in% "TREATMENT", !is.na(DSSTDTC)) |>30  arrange(STUDYID, USUBJID, desc(DSSTDTC), desc(DSSEQ)) |>31  distinct(STUDYID, USUBJID, .keep_all = TRUE) |>32  transmute(STUDYID, USUBJID, EOTDT = DSSTDTC, EOTDECOD = DSDECOD, EOTREAS = DSTERM)3334adsl <- dm |>35  left_join(last_study, by = c("STUDYID", "USUBJID")) |>36  left_join(last_trt, by = c("STUDYID", "USUBJID")) |>37  mutate(38    EOSSTT = case_when(39      EOSDECOD == "COMPLETED" ~ "COMPLETED",40      !is.na(EOSDECOD) ~ "DISCONTINUED",41      .default = "ONGOING"42    ),43    DCSREAS = if_else(EOSSTT == "DISCONTINUED", EOSREAS, NA_character_),44    EOTSTT = case_when(45      EOTDECOD == "COMPLETED" ~ "COMPLETED",46      !is.na(EOTDT) ~ "DISCONTINUED",47      .default = "ONGOING"48    ),49    DCTREAS = if_else(EOTSTT == "DISCONTINUED", EOTREAS, NA_character_),50    DCSREASP = if_else(EOTDECOD %in% "OTHER", EOTREAS, NA_character_)51  ) |>52  select(53    STUDYID, USUBJID, EOSDT, EOSDECOD, EOSREAS, EOSSTT, DCSREAS,54    EOTDT, EOTSTT, DCTREAS, DCSREASP55  )5657dir.create("/app/output", showWarnings = FALSE)58write_csv(adsl, "/app/output/adsl.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adsl-disposition (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 pl1011dm = pl.read_csv("/app/input/dm.csv", infer_schema=False)12ds = pl.read_csv("/app/input/ds.csv", infer_schema=False).with_columns(13    pl.col("DSSEQ").cast(pl.Int64, strict=False),14    pl.col("DSSTDTC").str.to_date(strict=False),15)1617# The last dated disposition event per track: latest date, highest sequence18# on a tie. The study track reads every epoch but TREATMENT; the treatment19# track reads only TREATMENT.20last_study = (21    ds.filter(22        (pl.col("DSCAT") == "DISPOSITION EVENT")23        & (pl.col("EPOCH") != "TREATMENT")24        & pl.col("DSSTDTC").is_not_null()25    )26    .sort(["DSSTDTC", "DSSEQ"], descending=True, nulls_last=True)27    .unique(["STUDYID", "USUBJID"], keep="first", maintain_order=True)28    .select("STUDYID", "USUBJID", EOSDT="DSSTDTC", EOSDECOD="DSDECOD", EOSREAS="DSTERM")29)3031last_trt = (32    ds.filter(33        (pl.col("DSCAT") == "DISPOSITION EVENT")34        & (pl.col("EPOCH") == "TREATMENT")35        & pl.col("DSSTDTC").is_not_null()36    )37    .sort(["DSSTDTC", "DSSEQ"], descending=True, nulls_last=True)38    .unique(["STUDYID", "USUBJID"], keep="first", maintain_order=True)39    .select("STUDYID", "USUBJID", EOTDT="DSSTDTC", EOTDECOD="DSDECOD", EOTREAS="DSTERM")40)4142adsl = (43    dm.join(last_study, on=["STUDYID", "USUBJID"], how="left", maintain_order="left")44    .join(last_trt, on=["STUDYID", "USUBJID"], how="left", maintain_order="left")45    .with_columns(46        EOSSTT=pl.when(pl.col("EOSDECOD") == "COMPLETED")47        .then(pl.lit("COMPLETED"))48        .when(pl.col("EOSDECOD").is_not_null())49        .then(pl.lit("DISCONTINUED"))50        .otherwise(pl.lit("ONGOING")),51        DCSREAS=pl.when(52            pl.col("EOSDECOD").is_not_null() & (pl.col("EOSDECOD") != "COMPLETED")53        )54        .then(pl.col("EOSREAS"))55        .otherwise(None),56        EOTSTT=pl.when(pl.col("EOTDECOD") == "COMPLETED")57        .then(pl.lit("COMPLETED"))58        .when(pl.col("EOTDT").is_not_null())59        .then(pl.lit("DISCONTINUED"))60        .otherwise(pl.lit("ONGOING")),61        DCTREAS=pl.when(62            pl.col("EOTDT").is_not_null()63            & (pl.col("EOTDECOD").fill_null("") != "COMPLETED")64        )65        .then(pl.col("EOTREAS"))66        .otherwise(None),67        DCSREASP=pl.when(pl.col("EOTDECOD") == "OTHER")68        .then(pl.col("EOTREAS"))69        .otherwise(None),70    )71    .select(72        "STUDYID",73        "USUBJID",74        "EOSDT",75        "EOSDECOD",76        "EOSREAS",77        "EOSSTT",78        "DCSREAS",79        "EOTDT",80        "EOTSTT",81        "DCTREAS",82        "DCSREASP",83    )84)8586Path("/app/output").mkdir(exist_ok=True)87adsl.write_csv("/app/output/adsl.csv")

1/* opensas reference solution for the yamaa benchmark adam-adsl-disposition.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 $1024;7  infile "/app/input/dm.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024.;9run;1011data ds;12  length STUDYID USUBJID DSCAT EPOCH DSDECOD DSTERM DSSTDTC $1024;13  infile "/app/input/ds.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024. DSSEQ DSCAT : $char1024. EPOCH : $char1024. DSDECOD : $char1024. DSTERM : $char1024. DSSTDTC : $char1024.;15run;1617proc sort data=ds(where=(DSCAT='DISPOSITION EVENT' and EPOCH ne 'TREATMENT' and DSSTDTC ne '')) out=ordered_study;18  by STUDYID USUBJID descending DSSTDTC descending DSSEQ;19run;20data lastds; set ordered_study; by STUDYID USUBJID; if first.USUBJID; run;2122proc sort data=ds(where=(DSCAT='DISPOSITION EVENT' and EPOCH='TREATMENT' and DSSTDTC ne '')) out=ordered_trt;23  by STUDYID USUBJID descending DSSTDTC descending DSSEQ;24run;25data lasttrt; set ordered_trt; by STUDYID USUBJID; if first.USUBJID; keep STUDYID USUBJID DSSTDTC DSDECOD DSTERM; run;2627proc sql;28  create table joined as29    select a.*, b.DSSTDTC as EOSDT, b.DSDECOD as EOSDECOD, b.DSTERM as EOSREAS,30           c.DSSTDTC as EOTDT, c.DSDECOD as EOTDECOD, c.DSTERM as EOTREAS31    from dm as a32    left join lastds as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID33    left join lasttrt as c on a.STUDYID=c.STUDYID and a.USUBJID=c.USUBJID;34quit;35data result;36  length EOSSTT $12 DCSREAS $1024 EOTSTT $12 DCTREAS $1024 DCSREASP $1024;37  set joined;38  if missing(EOSDT) then EOSSTT='ONGOING';39  else if EOSDECOD='COMPLETED' then EOSSTT='COMPLETED';40  else EOSSTT='DISCONTINUED';41  if EOSSTT='DISCONTINUED' then DCSREAS=EOSREAS;42  if missing(EOTDT) then EOTSTT='ONGOING';43  else if EOTDECOD='COMPLETED' then EOTSTT='COMPLETED';44  else EOTSTT='DISCONTINUED';45  if EOTSTT='DISCONTINUED' then DCTREAS=EOTREAS;46  if EOTDECOD='OTHER' then DCSREASP=EOTREAS;47run;4849proc sql;50  create table final as select STUDYID, USUBJID, EOSDT, EOSDECOD, EOSREAS, EOSSTT, DCSREAS, EOTDT, EOTSTT, DCTREAS, DCSREASP from result;51quit;52proc export data=final outfile="/app/output/adsl.csv" dbms=csv replace; run;