scripts/eqc_qa/parse_reports.py

#!/usr/bin/env python3
"""
parse_reports.py — extract TEXT only from each EQC QA notebook.

For every repo/**/*.ipynb (parsed as JSON, no nbformat dependency):
  - markdown cells  -> kept verbatim (prose: methodology, findings, verdicts;
                       headings preserved for section-aware chunking)
  - code cells      -> comment lines from source (prose intent) + TEXT outputs
                       (stream stdout/stderr, execute_result/display_data
                        'text/plain'). SKIP image/png/jpeg/svg/base64/raw data.

Filename encodes dataset + report type:
  <prefix>_<dataset_id>_<aspect>_q<NN>.ipynb
  e.g. satellite_satellite-sea-surface-temperature_consistency_q01
       -> dataset=satellite-sea-surface-temperature aspect=consistency q=q01

Dataset mapping: cross-reference dataset_id against the CDS/ADS/EWDS catalogue
(meta_harvest/{cds,ads,ewds}_enriched.json); exact -> fuzzy substring -> unmatched.

Outputs:
  eqc_qa/parsed/<report_id>.md
  eqc_qa/reports.jsonl  (manifest, one line per report)

templates/template.ipynb is a scaffold (not a dataset report): parsed for text
but flagged is_template and left dataset-unmatched.
"""
import json
import sys
import re
from pathlib import Path

ROOT = Path(__file__).resolve().parent
REPO = ROOT / "repo"
PARSED = ROOT / "parsed"
MANIFEST = ROOT / "reports.jsonl"
META = ROOT.parent / "meta_harvest"


def log(*a):
    print(*a, file=sys.stderr, flush=True)


# ── catalogue for dataset mapping ────────────────────────────────────────────
def load_catalogue() -> dict[str, str]:
    ids: dict[str, str] = {}
    for name, store in (("cds", "CDS"), ("ads", "ADS"), ("ewds", "EWDS")):
        p = META / f"{name}_enriched.json"
        if p.exists():
            for k in json.loads(p.read_text()):
                ids[k] = store
    return ids


def map_dataset(dataset_id: str, catalogue: dict[str, str]) -> tuple[str, str, str]:
    """Return (matched_id, store, confidence:{exact,fuzzy,unmatched})."""
    if not dataset_id:
        return "", "", "unmatched"
    if dataset_id in catalogue:
        return dataset_id, catalogue[dataset_id], "exact"
    # fuzzy: substring either direction (guard against trivially short ids)
    if len(dataset_id) >= 5:
        cands = [k for k in catalogue if dataset_id in k or k in dataset_id]
        if cands:
            best = min(cands, key=len)
            return best, catalogue[best], "fuzzy"
    return "", "", "unmatched"


# ── text extraction ──────────────────────────────────────────────────────────
def _src(cell) -> str:
    s = cell.get("source", "")
    return "".join(s) if isinstance(s, list) else s


def comment_lines(code: str) -> list[str]:
    out = []
    for ln in code.splitlines():
        st = ln.strip()
        if st.startswith("#") and not st.startswith("#!"):
            txt = st.lstrip("#").strip()
            if len(txt) >= 12 and not txt.startswith("%"):  # skip trivial / magics
                out.append(txt)
    return out


def text_outputs(cell) -> list[str]:
    out = []
    for o in cell.get("outputs", []):
        ot = o.get("output_type")
        if ot == "stream":
            t = o.get("text", "")
            out.append("".join(t) if isinstance(t, list) else t)
        elif ot in ("execute_result", "display_data"):
            data = o.get("data", {})
            tp = data.get("text/plain")
            if tp is not None:
                # skip pure object reprs like "<Figure ...>" / matplotlib handles
                s = "".join(tp) if isinstance(tp, list) else tp
                s = s.strip()
                if s and not re.fullmatch(r"<[^>]+>", s) and not s.startswith("<Figure"):
                    out.append(s)
        # image/png, image/jpeg, image/svg+xml, application/* -> skipped entirely
    return out


def parse_notebook(path: Path) -> tuple[str, str]:
    """Return (markdown_text, title)."""
    nb = json.loads(path.read_text(encoding="utf-8", errors="replace"))
    parts: list[str] = []
    for cell in nb.get("cells", []):
        ct = cell.get("cell_type")
        if ct == "markdown":
            txt = _src(cell).strip()
            if txt:
                parts.append(txt)
        elif ct == "code":
            src = _src(cell)
            cmts = comment_lines(src)
            if cmts:
                parts.append("\n".join(cmts))
            for to in text_outputs(cell):
                to = to.strip()
                if to and len(to) >= 8:
                    parts.append("```text\n" + to + "\n```")
    md = "\n\n".join(parts).strip()
    # title = first H1
    title = ""
    for ln in md.splitlines():
        if ln.startswith("# "):
            title = ln[2:].strip()
            break
    if not title:
        title = path.stem
    return md, title


# ── manifest build ───────────────────────────────────────────────────────────
def main() -> None:
    PARSED.mkdir(exist_ok=True)
    catalogue = load_catalogue()
    log(f"catalogue: {len(catalogue)} collection ids")

    nbs = sorted(REPO.rglob("*.ipynb"))
    log(f"parsing {len(nbs)} notebooks")

    records = []
    stats = {"exact": 0, "fuzzy": 0, "unmatched": 0}
    for nb in nbs:
        rel = nb.relative_to(REPO)
        category = rel.parts[0]
        report_id = nb.stem
        toks = report_id.split("_")
        is_template = len(toks) != 4
        if is_template:
            dataset_id, aspect_base, qnum = "", "", ""
        else:
            _prefix, dataset_id, aspect_base, qnum = toks
        aspect = f"{aspect_base}_{qnum}" if aspect_base else ""

        matched_id, store, conf = map_dataset(dataset_id, catalogue)
        if is_template:
            conf = "unmatched"
        stats[conf] += 1

        md, title = parse_notebook(nb)
        md_path = PARSED / f"{report_id}.md"
        md_path.write_text(md, encoding="utf-8")

        rec = {
            "report_id": report_id,
            "dataset_id": dataset_id,
            "matched_dataset_id": matched_id,
            "store": store,
            "match_confidence": conf,
            "category": category,
            "aspect": aspect,
            "aspect_base": aspect_base,
            "qnum": qnum,
            "title": title,
            "md_path": str(md_path.relative_to(ROOT)),
            "n_chars": len(md),
            "is_template": is_template,
            "src_path": str(rel),
        }
        records.append(rec)

    with open(MANIFEST, "w", encoding="utf-8") as f:
        for r in records:
            f.write(json.dumps(r, ensure_ascii=False) + "\n")

    reports = [r for r in records if not r["is_template"]]
    log(f"wrote {len(records)} manifest rows ({len(reports)} reports + "
        f"{len(records)-len(reports)} template) -> {MANIFEST}")
    log(f"mapping: exact={stats['exact']} fuzzy={stats['fuzzy']} unmatched={stats['unmatched']}")
    ndatasets = len({r['matched_dataset_id'] for r in reports if r['match_confidence'] != 'unmatched'})
    log(f"reports mapped to a known collection: "
        f"{sum(1 for r in reports if r['match_confidence']!='unmatched')}/{len(reports)} "
        f"across {ndatasets} unique collections")
    log(f"total chars: {sum(r['n_chars'] for r in records):,}")


if __name__ == "__main__":
    main()