Derive the new anti-cancer therapy start date

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-new-therapy (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)910adsl_raw <- read_csv(11  "/app/input/adsl.csv",12  col_types = cols(TRTSDT = col_date(), .default = col_character())13)14cm <- read_csv(15  "/app/input/cm.csv",16  col_types = cols(CMSTDTC_IMP = col_date(), .default = col_character())17)18pr <- read_csv(19  "/app/input/pr.csv",20  col_types = cols(PRSTDTC = col_date(), .default = col_character())21)2223# A qualifying medication starts on or after treatment start; a record24# with no start date is skipped. The completed start fills a year-month25# to the 15th, so the IMP column is the comparison date.26cm_min <- cm |>27  inner_join(select(adsl_raw, STUDYID, USUBJID, TRTSDT), by = c("STUDYID", "USUBJID")) |>28  filter(CMCAT == "ON TREATMENT", !is.na(CMSTDTC_IMP), CMSTDTC_IMP >= TRTSDT) |>29  group_by(STUDYID, USUBJID) |>30  summarise(CMNACTDT = min(CMSTDTC_IMP), .groups = "drop")3132# A qualifying procedure is cancer related and on treatment, also on or33# after treatment start.34pr_min <- pr |>35  inner_join(select(adsl_raw, STUDYID, USUBJID, TRTSDT), by = c("STUDYID", "USUBJID")) |>36  filter(37    PRCAT == "CANCER RELATED", PRSCAT == "ON TREATMENT",38    !is.na(PRSTDTC), PRSTDTC >= TRTSDT39  ) |>40  group_by(STUDYID, USUBJID) |>41  summarise(PRNACTDT = min(PRSTDTC), .groups = "drop")4243adsl <- adsl_raw |>44  left_join(cm_min, by = c("STUDYID", "USUBJID")) |>45  left_join(pr_min, by = c("STUDYID", "USUBJID")) |>46  mutate(47    NACTDT = case_when(48      !is.na(CMNACTDT) & !is.na(PRNACTDT) ~ pmin(CMNACTDT, PRNACTDT),49      !is.na(CMNACTDT) ~ CMNACTDT,50      !is.na(PRNACTDT) ~ PRNACTDT,51      .default = as.Date(NA)52    )53  ) |>54  mutate(55    NACTDY = as.integer(NACTDT - TRTSDT) + 1L,56    NACTFL = if_else(is.na(NACTDT), NA_character_, "Y")57  ) |>58  select(STUDYID, USUBJID, TRTSDT, NACTDT, NACTDY, NACTFL) |>59  arrange(USUBJID)6061dir.create("/app/output", showWarnings = FALSE)62write_csv(adsl, "/app/output/adsl.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adsl-new-therapy (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 pl1011adsl_raw = pl.read_csv("/app/input/adsl.csv", infer_schema=False, null_values="").with_columns(12    TRTSDT=pl.col("TRTSDT").str.to_date(strict=False),13)14cm = pl.read_csv("/app/input/cm.csv", infer_schema=False, null_values="").with_columns(15    CMSTDTC_IMP=pl.col("CMSTDTC_IMP").str.to_date(strict=False),16)17pr = pl.read_csv("/app/input/pr.csv", infer_schema=False, null_values="").with_columns(18    PRSTDTC=pl.col("PRSTDTC").str.to_date(strict=False),19)2021# A qualifying medication starts on or after treatment start; a record22# with no start date is skipped. The completed start fills a year-month23# to the 15th, so the IMP column is the comparison date.24cm_min = (25    cm.join(adsl_raw.select("STUDYID", "USUBJID", "TRTSDT"), on=["STUDYID", "USUBJID"], how="left")26    .filter(27        (pl.col("CMCAT") == "ON TREATMENT")28        & pl.col("CMSTDTC_IMP").is_not_null()29        & (pl.col("CMSTDTC_IMP") >= pl.col("TRTSDT"))30    )31    .group_by(["STUDYID", "USUBJID"])32    .agg(CMNACTDT=pl.col("CMSTDTC_IMP").min())33)3435# A qualifying procedure is cancer related and on treatment, also on or36# after treatment start.37pr_min = (38    pr.join(adsl_raw.select("STUDYID", "USUBJID", "TRTSDT"), on=["STUDYID", "USUBJID"], how="left")39    .filter(40        (pl.col("PRCAT") == "CANCER RELATED")41        & (pl.col("PRSCAT") == "ON TREATMENT")42        & pl.col("PRSTDTC").is_not_null()43        & (pl.col("PRSTDTC") >= pl.col("TRTSDT"))44    )45    .group_by(["STUDYID", "USUBJID"])46    .agg(PRNACTDT=pl.col("PRSTDTC").min())47)4849adsl = (50    adsl_raw.join(cm_min, on=["STUDYID", "USUBJID"], how="left")51    .join(pr_min, on=["STUDYID", "USUBJID"], how="left")52    .with_columns(53        NACTDT=pl.min_horizontal("CMNACTDT", "PRNACTDT"),54    )55    .with_columns(56        NACTDY=(pl.col("NACTDT") - pl.col("TRTSDT")).dt.total_days() + 1,57        NACTFL=pl.when(pl.col("NACTDT").is_not_null())58        .then(pl.lit("Y"))59        .otherwise(None),60    )61    .select("STUDYID", "USUBJID", "TRTSDT", "NACTDT", "NACTDY", "NACTFL")62    .sort("USUBJID")63)6465Path("/app/output").mkdir(parents=True, exist_ok=True)66adsl.write_csv("/app/output/adsl.csv", null_value="")

1/* opensas reference solution for the yamaa benchmark adam-adsl-new-therapy.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data adsl;6  length STUDYID USUBJID TRTSDT $1024;7  infile "/app/input/adsl.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. TRTSDT : $char1024.;9run;1011data cm;12  length STUDYID USUBJID CMCAT CMSCAT CMTRT CMSTDTC CMSTDTC_IMP $1024;13  infile "/app/input/cm.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024. CMSEQ CMCAT : $char1024. CMSCAT : $char1024. CMTRT : $char1024. CMSTDTC : $char1024. CMSTDTC_IMP : $char1024.;15run;1617data pr;18  length STUDYID USUBJID PRCAT PRSCAT PRTRT PRSTDTC $1024;19  infile "/app/input/pr.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;20  input STUDYID : $char1024. USUBJID : $char1024. PRSEQ PRCAT : $char1024. PRSCAT : $char1024. PRTRT : $char1024. PRSTDTC : $char1024.;21run;2223data medication;24  length therapy $10;25  set cm;26  if CMCAT='ON TREATMENT';27  /* Use the supplied completed date, including its collected corrections. */28  therapy='';29  if lengthn(CMSTDTC_IMP)>=10 then therapy=substr(CMSTDTC_IMP,1,10);30run;31data procedure;32  length therapy $10;33  set pr;34  if PRCAT='CANCER RELATED' and PRSCAT='ON TREATMENT';35  therapy=substr(PRSTDTC,1,10);36run;37data therapies; set medication procedure; keep STUDYID USUBJID therapy; run;38proc sql;39  create table firsttherapy as select a.STUDYID,a.USUBJID,min(b.therapy) as NACTDT from adsl as a inner join therapies as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID where a.TRTSDT ne '' and b.therapy ne '' and b.therapy>=a.TRTSDT group by a.STUDYID,a.USUBJID;40  create table joined as select a.*,b.NACTDT from adsl as a left join firsttherapy as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID;41quit;42data result;43  length NACTFL $1; set joined;44  NACTFL=''; NACTDY=.;45  if not missing(NACTDT) then do; NACTFL='Y'; NACTDY=input(NACTDT,yymmdd10.)-input(TRTSDT,yymmdd10.)+1; end;46run;4748proc sql;49  create table final as select STUDYID, USUBJID, TRTSDT, NACTDT, NACTDY, NACTFL from result;50quit;51proc export data=final outfile="/app/output/adsl.csv" dbms=csv replace; run;