Keep an Investigator Comment Exactly as Collected

1library(yamaa)23yamaa_spec("spec.yaml")$run()$output

1import yamaa23yamaa.spec("spec.yaml").run().output

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# A comment field that is empty, quoted or not, or holds only spaces17# counts as no comment collected; any other comment is kept as recorded.18adsl <- dm |>19  mutate(20    CMNT = if_else(grepl("\\S", COMMENT), COMMENT, NA_character_),21    CMNTFL = if_else(is.na(CMNT), "N", "Y")22  ) |>23  select(STUDYID, USUBJID, CMNT, CMNTFL) |>24  arrange(USUBJID)2526dir.create("/app/output", showWarnings = FALSE)27write_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 1.67"""Create ADSL (one record per subject) from DM.89CMNT carries the investigator comment exactly as recorded; CMNTFL is10"Y" when a comment was collected and "N" when none was. A comment11field that is empty (quoted or not) or holds only spaces counts as no12comment.13"""1415import csv16import os1718INPUT_DIR = "/app/input"19OUTPUT_DIR = "/app/output"2021FIELDNAMES = ["STUDYID", "USUBJID", "CMNT", "CMNTFL"]222324def main():25    with open(26        os.path.join(INPUT_DIR, "dm.csv"), newline="", encoding="utf-8"27    ) as handle:28        dm_rows = list(csv.DictReader(handle))2930    adsl_rows = []31    for row in dm_rows:32        comment = row.get("COMMENT") or ""33        collected = comment.strip() != ""34        adsl_rows.append(35            {36                "STUDYID": row["STUDYID"],37                "USUBJID": row["USUBJID"],38                "CMNT": comment if collected else "",39                "CMNTFL": "Y" if collected else "N",40            }41        )4243    os.makedirs(OUTPUT_DIR, exist_ok=True)44    with open(45        os.path.join(OUTPUT_DIR, "adsl.csv"),46        "w",47        newline="",48        encoding="utf-8",49    ) as handle:50        writer = csv.DictWriter(handle, fieldnames=FIELDNAMES)51        writer.writeheader()52        writer.writerows(adsl_rows)535455if __name__ == "__main__":56    main()

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, so each field's length7   is counted as it is read. An empty field, quoted or not, has length8   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. A69   field of only spaces counts as no comment, so it has length zero too. */70data dm;71  set dm;72  if lengthn(COMMENT) = 0 then CMNTLEN = 0;73run;7475proc sql;76  create table adsl as77  select STUDYID, USUBJID,78         case when CMNTLEN > 0 then COMMENT else "" end as CMNT length=1000,79         case when CMNTLEN > 0 then "Y" else "N" end as CMNTFL length=1,80         CMNTLEN81  from dm82  order by STUDYID, USUBJID;83quit;8485/* Write the file directly: the comment quoted, with its quotation marks86   doubled, at its recorded length. */87data _null_;88  set adsl;89  file "/app/output/adsl.csv";90  length QUOTED $2000 OUTLINE $2200;91  if _n_ = 1 then put "STUDYID,USUBJID,CMNT,CMNTFL";92  if CMNTLEN = 0 then93    OUTLINE = trim(STUDYID) || "," || trim(USUBJID) || ",," || CMNTFL;94  else do;95    QUOTED = tranwrd(CMNT, '"', '""');96    QLEN = CMNTLEN + countc(CMNT, '"');97    OUTLINE = trim(STUDYID) || "," || trim(USUBJID) || ',"'98              || substr(QUOTED, 1, QLEN) || '",' || CMNTFL;99  end;100  put OUTLINE;101run;