Tablinum-2: the Lite-Beam engram, release 2 (card, code, recipes, 9 released tables)
901f964 verified | """statpearls_chunk.py NXML_DIR OUT.parquet - StatPearls (NCBI Bookshelf NBK430685 tarball, ~9.3k articles) -> engram passages | |
| (10-20, health table). One passage per ~WORDS words of a section, prefixed "Article — Section: " like chunk.py; bold-only | |
| paragraphs become sub-headings. Same schema as chunk.py; file_idx from OUT's name AAA_BB. Not redistributable: local use only.""" | |
| import sys, re, os, glob | |
| import xml.etree.ElementTree as ET | |
| import pyarrow as pa, pyarrow.parquet as pq | |
| WORDS, MIN_WORDS = 140, 12 | |
| src, dst = sys.argv[1], sys.argv[2] | |
| a, b = re.search(r"(\d+)_(\d+)\.parquet$", dst).groups(); fidx = int(b) + 100 * int(a) | |
| txt = lambda e: re.sub(r"\s+", " ", "".join(e.itertext())).strip() | |
| cols = {"pid": [], "page_id": [], "title": [], "section": [], "text": []}; n = arts = 0 | |
| def emit(title, sec, words, nbk): | |
| global n | |
| for i in range(0, len(words), WORDS): | |
| part = words[i:i + WORDS + 20] if len(words) - i <= WORDS + 20 else words[i:i + WORDS] | |
| if len(part) >= MIN_WORDS: | |
| cols["pid"].append((fidx << 32) | n); cols["page_id"].append(nbk); cols["title"].append(title); cols["section"].append(sec) | |
| cols["text"].append(f"{title} — {sec}: " + " ".join(part)); n += 1 | |
| if len(words) - i <= WORDS + 20: | |
| break | |
| for f in sorted(glob.glob(f"{src}/**/*.nxml", recursive=True)): | |
| try: | |
| root = ET.parse(f).getroot() | |
| except ET.ParseError: | |
| continue | |
| t = root.find(".//title"); title = txt(t) if t is not None else os.path.basename(f)[:-5] | |
| nbk = int((re.search(r"NBK(\d+)", f) or re.search(r"(\d+)", "0")).group(1)); arts += 1 | |
| for sec in root.iter("sec"): | |
| st = sec.find("title"); sname = txt(st) if st is not None else "" | |
| if sname.lower() in ("references", "review questions", "continuing education activity"): | |
| continue | |
| buf, sub = [], sname | |
| for ch in sec: | |
| if ch.tag == "p" and len(ch) == 1 and ch[0].tag == "bold" and not (ch[0].tail or "").strip() and not (ch.text or "").strip(): | |
| emit(title, sub, buf, nbk); buf = []; sub = f"{sname} — {txt(ch)}" | |
| elif ch.tag in ("p", "list", "table-wrap"): | |
| buf += txt(ch).split() | |
| emit(title, sub, buf, nbk) | |
| pq.write_table(pa.table(cols), dst + ".tmp", compression="zstd", row_group_size=4096); os.replace(dst + ".tmp", dst) | |
| print(src, "articles", arts, "passages", n, flush=True) | |