@oriro/orirocli 0.1.8 → 0.1.9

package/skills/graphify/dedup.py

@@ -0,0 +1,429 @@
+"""Entity deduplication pipeline for graphify knowledge graphs.
+
+Pipeline: exact normalization → entropy gate → MinHash/LSH blocking →
+Jaro-Winkler verification → same-community boost → union-find merge.
+"""
+from __future__ import annotations
+import math
+import re
+import unicodedata
+from collections import defaultdict
+
+from datasketch import MinHash, MinHashLSH
+from rapidfuzz.distance import JaroWinkler
+
+
+# ── helpers ───────────────────────────────────────────────────────────────────
+
+def _norm(label: str) -> str:
+    """Lowercase + collapse non-alphanumeric runs to space (Unicode-aware)."""
+    label = unicodedata.normalize("NFKC", label)
+    return re.sub(r"[\W_]+", " ", label.casefold(), flags=re.UNICODE).strip()
+
+
+def _entropy(label: str) -> float:
+    """Shannon entropy in bits/char of the normalised label."""
+    s = _norm(label)
+    if not s:
+        return 0.0
+    freq: dict[str, int] = defaultdict(int)
+    for ch in s:
+        freq[ch] += 1
+    n = len(s)
+    return -sum((c / n) * math.log2(c / n) for c in freq.values())
+
+
+def _shingles(text: str, k: int = 3) -> set[str]:
+    """Return k-gram character shingles of text."""
+    if len(text) < k:
+        return {text}
+    return {text[i : i + k] for i in range(len(text) - k + 1)}
+
+
+def _make_minhash(text: str, num_perm: int = 128) -> MinHash:
+    # Strip spaces so "graph extractor" and "graphextractor" share shingles
+    m = MinHash(num_perm=num_perm)
+    for shingle in _shingles(text.replace(" ", "")):
+        m.update(shingle.encode("utf-8"))
+    return m
+
+
+# Matches labels whose trailing token is a version/variant suffix:
+# digits optionally followed by letters (chip SKUs: ASR1603, M1, Cortex-A55)
+# or 2+ letters (codename revisions: cranelr vs cranel).
+# Requires the stem to end in a letter so plain words don't accidentally match.
+_VARIANT_SUFFIX = re.compile(r"^(.*[a-z])([0-9]+[a-z]*|[a-z]{2,})$")
+
+
+def _is_variant_pair(a: str, b: str) -> bool:
+    """True if a and b are sibling model/SKU variants (same stem, different suffix).
+
+    Only applied to short labels (< 12 chars); long labels go through JW normally.
+    """
+    if a == b:
+        return False
+    if max(len(a), len(b)) >= 12:
+        return False
+    ma, mb = _VARIANT_SUFFIX.match(a), _VARIANT_SUFFIX.match(b)
+    if not (ma and mb):
+        return False
+    return ma.group(1) == mb.group(1) and ma.group(2) != mb.group(2)
+
+
+def _short_label_blocked(a: str, b: str, jw_score: float) -> bool:
+    """Block fuzzy merge for short labels unless it's a same-length single-char substitution.
+
+    Insertions/deletions on short strings (cranel/cranelr, M1/M1 Pro) produce
+    high Jaro-Winkler scores due to the prefix bonus but are almost never true
+    duplicates — they're abbreviations or variants.
+    """
+    if max(len(a), len(b)) >= 12:
+        return False
+    from rapidfuzz.distance import DamerauLevenshtein
+    # Allow only same-length single-char substitutions (true typos like "Extractor"/"Extractar").
+    # Block length-differing pairs regardless of score.
+    if jw_score >= 97.0 and len(a) == len(b) and DamerauLevenshtein.distance(a, b) <= 1:
+        return False
+    return True
+
+
+# ── union-find ────────────────────────────────────────────────────────────────
+
+class _UF:
+    def __init__(self) -> None:
+        self._parent: dict[str, str] = {}
+
+    def find(self, x: str) -> str:
+        self._parent.setdefault(x, x)
+        while self._parent[x] != x:
+            self._parent[x] = self._parent[self._parent[x]]
+            x = self._parent[x]
+        return x
+
+    def union(self, x: str, y: str) -> None:
+        self._parent.setdefault(x, x)
+        self._parent.setdefault(y, y)
+        rx, ry = self.find(x), self.find(y)
+        if rx != ry:
+            self._parent[ry] = rx
+
+    def components(self) -> dict[str, list[str]]:
+        groups: dict[str, list[str]] = defaultdict(list)
+        for x in self._parent:
+            groups[self.find(x)].append(x)
+        return dict(groups)
+
+
+# ── constants ─────────────────────────────────────────────────────────────────
+
+_ENTROPY_THRESHOLD = 2.5
+_LSH_THRESHOLD = 0.7
+_MERGE_THRESHOLD = 92.0     # rapidfuzz normalized_similarity * 100
+_COMMUNITY_BOOST = 5.0      # score bonus when both nodes share community
+_NUM_PERM = 128
+_CHUNK_SUFFIX = re.compile(r"_c\d+$")
+
+
+# ── main entry point ──────────────────────────────────────────────────────────
+
+def deduplicate_entities(
+    nodes: list[dict],
+    edges: list[dict],
+    *,
+    communities: dict[str, int],
+    dedup_llm_backend: str | None = None,
+) -> tuple[list[dict], list[dict]]:
+    """Deduplicate near-identical entities in a knowledge graph.
+
+    Args:
+        nodes: list of node dicts with at minimum {"id": str, "label": str}
+        edges: list of edge dicts with {"source": str, "target": str, ...}
+        communities: mapping of node_id -> community_id (from cluster())
+        dedup_llm_backend: if set, use LLM to resolve ambiguous pairs
+
+    Returns:
+        (deduped_nodes, deduped_edges) with edges rewired to survivors
+    """
+    # Guard: cross-project dedup is not supported — nodes from different repos
+    # share label names by coincidence and must never be merged by string similarity.
+    # If you need to dedup a global graph, run deduplicate_entities per-repo first.
+    repos_seen = {n.get("repo") for n in nodes if n.get("repo")}
+    if len(repos_seen) > 1:
+        raise ValueError(
+            f"deduplicate_entities: nodes span multiple repos {sorted(repos_seen)!r}. "
+            f"Cross-project dedup is disabled — run dedup per-repo before merging."
+        )
+
+    if len(nodes) <= 1:
+        return nodes, edges
+
+    # Pre-deduplicate: keep first occurrence of each id
+    seen_ids: dict[str, dict] = {}
+    for node in nodes:
+        nid = node.get("id", "")
+        if nid and nid not in seen_ids:
+            seen_ids[nid] = node
+    unique_nodes = list(seen_ids.values())
+
+    if len(unique_nodes) <= 1:
+        return unique_nodes, edges
+
+    # ── pass 1: exact normalization ───────────────────────────────────────────
+    norm_to_nodes: dict[str, list[dict]] = defaultdict(list)
+    for node in unique_nodes:
+        key = _norm(node.get("label", node.get("id", "")))
+        if key:
+            norm_to_nodes[key].append(node)
+
+    uf = _UF()
+    exact_merges = 0
+    for key, group in norm_to_nodes.items():
+        if len(group) <= 1:
+            continue
+        # Partition by source_file — only merge within the same file in Pass 1.
+        # Cross-file matches fall through to Pass 2 fuzzy matching.
+        by_file: dict[str, list[dict]] = defaultdict(list)
+        for node in group:
+            sf = node.get("source_file") or ""
+            by_file[sf].append(node)
+        for sf, file_group in by_file.items():
+            if not sf:
+                # No source_file — cannot prove same symbol; skip to avoid
+                # collapsing distinct nodes that happen to share a label (#1178).
+                continue
+            if len(file_group) > 1:
+                winner = _pick_winner(file_group)
+                for node in file_group:
+                    uf.union(winner["id"], node["id"])
+                exact_merges += len(file_group) - 1
+
+    # ── pass 2: MinHash/LSH + Jaro-Winkler (high-entropy nodes only) ─────────
+    candidates: list[dict] = []
+    seen_norms: set[str] = set()
+    for node in unique_nodes:
+        key = _norm(node.get("label", node.get("id", "")))
+        if key and key not in seen_norms:
+            seen_norms.add(key)
+            if _entropy(node.get("label", "")) >= _ENTROPY_THRESHOLD:
+                candidates.append(node)
+
+    fuzzy_merges = 0
+    if len(candidates) >= 2:
+        lsh = MinHashLSH(threshold=_LSH_THRESHOLD, num_perm=_NUM_PERM)
+        minhashes: dict[str, MinHash] = {}
+
+        for node in candidates:
+            norm_label = _norm(node.get("label", node.get("id", "")))
+            m = _make_minhash(norm_label)
+            minhashes[node["id"]] = m
+            try:
+                lsh.insert(node["id"], m)
+            except ValueError:
+                pass  # duplicate key in LSH — already inserted
+
+        for node in candidates:
+            node_id = node["id"]
+            norm_label = _norm(node.get("label", node.get("id", "")))
+            neighbors = lsh.query(minhashes[node_id])
+
+            for neighbor_id in neighbors:
+                if neighbor_id == node_id:
+                    continue
+                if uf.find(node_id) == uf.find(neighbor_id):
+                    continue
+
+                neighbor = next((n for n in candidates if n["id"] == neighbor_id), None)
+                if neighbor is None:
+                    continue
+
+                neighbor_norm = _norm(neighbor.get("label", neighbor.get("id", "")))
+                score = JaroWinkler.normalized_similarity(norm_label, neighbor_norm) * 100
+
+                if _is_variant_pair(norm_label, neighbor_norm):
+                    continue
+                if _short_label_blocked(norm_label, neighbor_norm, score):
+                    continue
+
+                c1 = communities.get(node_id)
+                c2 = communities.get(neighbor_id)
+                if (c1 is not None and c2 is not None and c1 == c2
+                        and min(len(norm_label), len(neighbor_norm)) >= 12):
+                    score += _COMMUNITY_BOOST
+
+                if score >= _MERGE_THRESHOLD:
+                    # Identical labels across different source files almost always
+                    # means same-named-but-different symbols (trait impls, wrapper
+                    # methods, common type names). Mirror Pass 1's source_file
+                    # partition for this sub-case. (#1046, leaks #895's fix)
+                    if norm_label == neighbor_norm:
+                        sf_a = node.get("source_file") or ""
+                        sf_b = neighbor.get("source_file") or ""
+                        if sf_a != sf_b:
+                            continue
+                    all_group = norm_to_nodes.get(norm_label, [node]) + \
+                                norm_to_nodes.get(neighbor_norm, [neighbor])
+                    winner = _pick_winner(all_group)
+                    uf.union(winner["id"], node_id)
+                    uf.union(winner["id"], neighbor_id)
+                    fuzzy_merges += 1
+
+    # ── pass 3: LLM tiebreaker for ambiguous pairs (opt-in) ──────────────────
+    if dedup_llm_backend is not None:
+        _llm_tiebreak(candidates, uf, communities, backend=dedup_llm_backend)
+
+    # ── build remap table from union-find components ──────────────────────────
+    components = uf.components()
+    remap: dict[str, str] = {}
+
+    for root, members in components.items():
+        if len(members) == 1:
+            continue
+        group_nodes = [n for n in unique_nodes if n["id"] in members]
+        winner = _pick_winner(group_nodes) if group_nodes else {"id": root}
+        winner_id = winner["id"]
+        for member in members:
+            if member != winner_id:
+                remap[member] = winner_id
+
+    # ── apply remap ───────────────────────────────────────────────────────────
+    if not remap:
+        return unique_nodes, edges
+
+    total = len(remap)
+    msg = f"[graphify] Deduplicated {total} node(s)"
+    if exact_merges:
+        msg += f" ({exact_merges} exact"
+        if fuzzy_merges:
+            msg += f", {fuzzy_merges} fuzzy"
+        msg += ")"
+    print(msg + ".", flush=True)
+
+    deduped_nodes = [n for n in unique_nodes if n["id"] not in remap]
+    deduped_edges = []
+    for edge in edges:
+        e = dict(edge)
+        # Tolerate "from"/"to" keys from LLM backends that don't follow the
+        # schema exactly — build_from_json normalises later but dedup runs
+        # first so bracket access would KeyError here (#803).
+        # Use explicit key presence check (not `or`) so empty-string src/tgt
+        # aren't silently replaced by the fallback key.
+        src = e["source"] if "source" in e else e.get("from")
+        tgt = e["target"] if "target" in e else e.get("to")
+        if src is None or tgt is None:
+            continue
+        e["source"] = remap.get(src, src)
+        e["target"] = remap.get(tgt, tgt)
+        # Remove legacy keys so they don't leak into edge attrs in graph.json.
+        e.pop("from", None)
+        e.pop("to", None)
+        if e["source"] != e["target"]:
+            deduped_edges.append(e)
+
+    return deduped_nodes, deduped_edges
+
+
+def _pick_winner(nodes: list[dict]) -> dict:
+    """Pick the canonical survivor: prefer no chunk suffix, then shorter ID."""
+    if not nodes:
+        raise ValueError("Cannot pick winner from empty list")
+
+    def _score(n: dict) -> tuple[int, int]:
+        has_suffix = bool(_CHUNK_SUFFIX.search(n["id"]))
+        return (1 if has_suffix else 0, len(n["id"]))
+
+    return min(nodes, key=_score)
+
+
+def _llm_tiebreak(
+    candidates: list[dict],
+    uf: _UF,
+    communities: dict[str, int],
+    *,
+    backend: str,
+    batch_size: int = 30,
+    low: float = 75.0,
+    high: float = 92.0,
+) -> None:
+    """Batch-resolve ambiguous pairs (score in [low, high)) via LLM."""
+    try:
+        from graphify.llm import BACKENDS, _format_backend_env_keys, _get_backend_api_key
+        if backend not in BACKENDS:
+            print(f"[graphify] --dedup-llm: unknown backend {backend!r}, skipping LLM tiebreaker.", flush=True)
+            return
+        if not _get_backend_api_key(backend):
+            env_keys = _format_backend_env_keys(backend)
+            print(f"[graphify] --dedup-llm: {env_keys} not set, skipping LLM tiebreaker.", flush=True)
+            return
+    except ImportError:
+        return
+
+    ambiguous: list[tuple[dict, dict, float]] = []
+    for i, node in enumerate(candidates):
+        norm_i = _norm(node.get("label", node.get("id", "")))
+        for j in range(i + 1, len(candidates)):
+            neighbor = candidates[j]
+            if uf.find(node["id"]) == uf.find(neighbor["id"]):
+                continue
+            norm_j = _norm(neighbor.get("label", neighbor.get("id", "")))
+            score = JaroWinkler.normalized_similarity(norm_i, norm_j) * 100
+            if _is_variant_pair(norm_i, norm_j):
+                continue
+            if _short_label_blocked(norm_i, norm_j, score):
+                continue
+            c1 = communities.get(node["id"])
+            c2 = communities.get(neighbor["id"])
+            if (c1 is not None and c2 is not None and c1 == c2
+                    and min(len(norm_i), len(norm_j)) >= 12):
+                score += _COMMUNITY_BOOST
+            if low <= score < high:
+                ambiguous.append((node, neighbor, score))
+
+    if not ambiguous:
+        return
+
+    try:
+        from graphify.llm import _call_llm
+    except ImportError as exc:
+        # F-038: previously this silent fallback hid the fact that `_call_llm`
+        # didn't exist in `graphify.llm` at all, so `--dedup-llm` was a no-op.
+        # Surface the import failure so future regressions are visible.
+        print(
+            f"[graphify] --dedup-llm: cannot import _call_llm ({exc}); skipping LLM tiebreaker.",
+            flush=True,
+        )
+        return
+
+    for batch_start in range(0, len(ambiguous), batch_size):
+        batch = ambiguous[batch_start : batch_start + batch_size]
+        pairs_text = "\n".join(
+            f"{i+1}. \"{a['label']}\" vs \"{b['label']}\""
+            for i, (a, b, _) in enumerate(batch)
+        )
+        prompt = (
+            "For each pair below, answer only 'yes' or 'no': are they the same real-world concept?\n\n"
+            f"{pairs_text}\n\n"
+            "Reply with one line per pair: '1. yes', '2. no', etc."
+        )
+        try:
+            response = _call_llm(prompt, backend=backend, max_tokens=200)
+            lines = response.strip().splitlines()
+            for line in lines:
+                line = line.strip()
+                if not line:
+                    continue
+                parts = line.split(".", 1)
+                if len(parts) != 2:
+                    continue
+                try:
+                    idx = int(parts[0].strip()) - 1
+                except ValueError:
+                    continue
+                if 0 <= idx < len(batch):
+                    answer = parts[1].strip().lower()
+                    if answer.startswith("yes"):
+                        a, b, _ = batch[idx]
+                        winner = _pick_winner([a, b])
+                        uf.union(winner["id"], a["id"])
+                        uf.union(winner["id"], b["id"])
+        except Exception as exc:
+            print(f"[graphify] --dedup-llm batch failed: {exc}", flush=True)