Keep an Investigator Comment Exactly as Collected

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-investigator-comment (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  trim_ws = FALSE14)1516# An empty comment field, quoted or not, counts as no comment collected,17# while a field holding only spaces is still a comment and the spaces18# are kept.19adsl <- dm |>20  mutate(21    CMNT = na_if(COMMENT, ""),22    CMNTFL = if_else(is.na(CMNT), "N", "Y")23  ) |>24  select(STUDYID, USUBJID, CMNT, CMNTFL) |>25  arrange(USUBJID)2627dir.create("/app/output", showWarnings = FALSE)28write_csv(adsl, "/app/output/adsl.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adsl-investigator-comment (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, null_values="")1213# An empty comment field, quoted or not, counts as no comment collected,14# while a field holding only spaces is still a comment and the spaces15# are kept. Reading with null_values="" turns both empty forms into16# null and keeps spaces as-is.17adsl = (18    dm.with_columns(19        CMNT=pl.col("COMMENT"),20        CMNTFL=pl.when(pl.col("COMMENT").is_null())21        .then(pl.lit("N"))22        .otherwise(pl.lit("Y")),23    )24    .select("STUDYID", "USUBJID", "CMNT", "CMNTFL")25    .sort("USUBJID")26)2728Path("/app/output").mkdir(parents=True, exist_ok=True)29adsl.write_csv("/app/output/adsl.csv", null_value="")

1/* opensas reference solution for the yamaa benchmark adam-adsl-investigator-comment.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45/* Read DM line by line and split the fields here: a quoted comment can hold6   commas, doubled quotation marks, and line breaks, and a comment of only7   spaces keeps its spaces, so each field's length is counted as it is8   read. An empty field, quoted or not, has length zero. */9data dm;10  infile "/app/input/dm.csv" firstobs=2 truncover;11  length STUDYID $20 USUBJID $40 COMMENT $1000 FIELD $1000 CH $1;12  retain STUDYID USUBJID COMMENT FIELD "" CMNTLEN FLEN NFIELD INQUOTE 0;13  keep STUDYID USUBJID COMMENT CMNTLEN;14  input;15  if lengthn(_infile_) = 0 and not INQUOTE then delete;16  RECLEN = lengthc(_infile_);17  do I = 1 to RECLEN;18    CH = substr(_infile_, I, 1);19    if INQUOTE and CH = '"' then do;20      /* A doubled quotation mark inside quotes is one mark of the value. */21      if I < RECLEN and substr(_infile_, I + 1, 1) = '"' then do;22        link addchar;23        I + 1;24      end;25      else INQUOTE = 0;26    end;27    else if not INQUOTE and CH = '"' then INQUOTE = 1;28    else if not INQUOTE and CH = "," then link endfield;29    else link addchar;30  end;3132  /* A line break inside quotes is part of the comment; anywhere else it33     ends the record. */34  if INQUOTE then do;35    CH = '0A'x;36    link addchar;37  end;38  else do;39    link endfield;40    output;41    call missing(STUDYID, USUBJID, COMMENT);42    CMNTLEN = 0;43    NFIELD = 0;44  end;45  return;4647/* Append one character, a space included, to the field being read. */48addchar:49  if FLEN = 0 then FIELD = CH;50  else FIELD = substr(FIELD, 1, FLEN) || CH;51  FLEN + 1;52  return;5354/* Store the field just read under its column. */55endfield:56  NFIELD + 1;57  if NFIELD = 1 then STUDYID = FIELD;58  else if NFIELD = 2 then USUBJID = FIELD;59  else if NFIELD = 3 then do;60    COMMENT = FIELD;61    CMNTLEN = FLEN;62  end;63  FIELD = "";64  FLEN = 0;65  return;66run;6768/* CMNT is the comment as recorded, CMNTFL Y when one was collected. */69proc sql;70  create table adsl as71  select STUDYID, USUBJID,72         case when CMNTLEN > 0 then COMMENT else "" end as CMNT length=1000,73         case when CMNTLEN > 0 then "Y" else "N" end as CMNTFL length=1,74         CMNTLEN75  from dm76  order by STUDYID, USUBJID;77quit;7879/* PROC EXPORT would drop the spaces of a comment of only spaces, so write80   the file directly: the comment quoted, with its quotation marks doubled,81   at its recorded length. */82data _null_;83  set adsl;84  file "/app/output/adsl.csv";85  length QUOTED $2000 OUTLINE $2200;86  if _n_ = 1 then put "STUDYID,USUBJID,CMNT,CMNTFL";87  if CMNTLEN = 0 then88    OUTLINE = trim(STUDYID) || "," || trim(USUBJID) || ",," || CMNTFL;89  else do;90    QUOTED = tranwrd(CMNT, '"', '""');91    QLEN = CMNTLEN + countc(CMNT, '"');92    OUTLINE = trim(STUDYID) || "," || trim(USUBJID) || ',"'93              || substr(QUOTED, 1, QLEN) || '",' || CMNTFL;94  end;95  put OUTLINE;96run;