@oriro/orirocli 0.1.7 → 0.1.9

package/skills/graphify/diagnostics.py

@@ -0,0 +1,390 @@
+"""Read-only diagnostics for MultiDiGraph readiness."""
+
+from __future__ import annotations
+
+import json
+import re
+from collections import Counter, defaultdict
+from copy import deepcopy
+from pathlib import Path
+from typing import Any
+
+import networkx as nx
+
+
+_SUPPRESSION_DECL_RE = re.compile(r"^\s*(?P<name>seen_[A-Za-z0-9_]+)\s*[:=]")
+_TYPE_TUPLE_RE = re.compile(r"set\[tuple\[(?P<inside>[^\]]+)\]\]")
+
+
+def _safe_text(value: Any) -> str:
+    if value is None:
+        return ""
+    if isinstance(value, (str, int, float, bool)):
+        return str(value)
+    return json.dumps(value, sort_keys=True, default=str, ensure_ascii=False)
+
+
+def _edge_list(extraction: dict[str, Any]) -> list[Any]:
+    edges = extraction.get("edges")
+    if edges is None:
+        edges = extraction.get("links")
+    return edges if isinstance(edges, list) else []
+
+
+def _node_ids(extraction: dict[str, Any]) -> set[str]:
+    nodes = extraction.get("nodes", [])
+    if not isinstance(nodes, list):
+        return set()
+    return {
+        str(node["id"])
+        for node in nodes
+        if isinstance(node, dict) and "id" in node and node.get("id") is not None
+    }
+
+
+def _canonical_edge(edge: Any) -> dict[str, str]:
+    if not isinstance(edge, dict):
+        return {
+            "source": "",
+            "target": "",
+            "relation": "",
+            "confidence": "",
+            "source_file": "",
+            "source_location": "",
+            "context": "",
+            "_invalid": "non_object_edge",
+        }
+    source = edge.get("source", edge.get("from"))
+    target = edge.get("target", edge.get("to"))
+    return {
+        "source": _safe_text(source),
+        "target": _safe_text(target),
+        "relation": _safe_text(edge.get("relation")),
+        "confidence": _safe_text(edge.get("confidence")),
+        "source_file": _safe_text(edge.get("source_file")),
+        "source_location": _safe_text(edge.get("source_location")),
+        "context": _safe_text(edge.get("context")),
+        "_invalid": "",
+    }
+
+
+def _exact_signature(edge: Any) -> str:
+    if not isinstance(edge, dict):
+        return "<non-object>"
+    normalized = dict(edge)
+    if "source" not in normalized and "from" in normalized:
+        normalized["source"] = normalized["from"]
+    if "target" not in normalized and "to" in normalized:
+        normalized["target"] = normalized["to"]
+    normalized.pop("from", None)
+    normalized.pop("to", None)
+    return json.dumps(
+        normalized,
+        sort_keys=True,
+        default=str,
+        ensure_ascii=False,
+        separators=(",", ":"),
+    )
+
+
+def _count_extra(counter: Counter[Any]) -> int:
+    return sum(count - 1 for count in counter.values() if count > 1)
+
+
+def _variant_group_count(
+    grouped_edges: dict[tuple[str, str], list[dict[str, str]]],
+    field: str,
+    *,
+    relation_sensitive: bool = False,
+) -> int:
+    groups = 0
+    for edges in grouped_edges.values():
+        if relation_sensitive:
+            by_relation: dict[str, set[str]] = defaultdict(set)
+            for edge in edges:
+                by_relation[edge["relation"]].add(edge[field])
+            groups += sum(1 for values in by_relation.values() if len(values) > 1)
+        elif len({edge[field] for edge in edges}) > 1:
+            groups += 1
+    return groups
+
+
+def _tuple_arity_from_annotation(line: str) -> int:
+    match = _TYPE_TUPLE_RE.search(line)
+    if not match:
+        return 0
+    inside = match.group("inside").strip()
+    if not inside:
+        return 0
+    return inside.count(",") + 1
+
+
+def scan_producer_suppression_sites(path: str | Path) -> dict[str, Any]:
+    """Find likely `seen_*` producer-suppression sets in an extractor file."""
+    source_path = Path(path)
+    if not source_path.exists():
+        return {
+            "path": str(source_path),
+            "total_sites": 0,
+            "sites": [],
+            "error": "file not found",
+        }
+
+    sites: list[dict[str, Any]] = []
+    lines = source_path.read_text(encoding="utf-8").splitlines()
+    for lineno, line in enumerate(lines, start=1):
+        match = _SUPPRESSION_DECL_RE.match(line)
+        if not match:
+            continue
+        sites.append(
+            {
+                "line": lineno,
+                "name": match.group("name"),
+                "tuple_arity": _tuple_arity_from_annotation(line),
+                "sample": line.strip()[:120],
+            }
+        )
+
+    return {
+        "path": str(source_path),
+        "total_sites": len(sites),
+        "sites": sites,
+        "error": "",
+    }
+
+
+def diagnose_extraction(
+    extraction: dict[str, Any],
+    *,
+    directed: bool = True,
+    root: str | Path | None = None,
+    max_examples: int = 5,
+    extract_path: str | Path | None = None,
+) -> dict[str, Any]:
+    """Summarize same-endpoint edge-collapse risk for one JSON graph/extraction dict."""
+    from graphify.build import build_from_json
+
+    node_ids = _node_ids(extraction)
+    raw_edges = _edge_list(extraction)
+    canonical_edges = [_canonical_edge(edge) for edge in raw_edges]
+
+    exact_counts: Counter[str] = Counter(_exact_signature(edge) for edge in raw_edges)
+    directed_pairs: Counter[tuple[str, str]] = Counter()
+    undirected_pairs: Counter[tuple[str, str]] = Counter()
+    grouped: dict[tuple[str, str], list[dict[str, str]]] = defaultdict(list)
+
+    non_object_edges = 0
+    missing_endpoint_edges = 0
+    dangling_endpoint_edges = 0
+    self_loop_edges = 0
+    valid_candidate_edges = 0
+
+    for edge in canonical_edges:
+        if edge["_invalid"]:
+            non_object_edges += 1
+            continue
+        source = edge["source"]
+        target = edge["target"]
+        if not source or not target:
+            missing_endpoint_edges += 1
+            continue
+        if source not in node_ids or target not in node_ids:
+            dangling_endpoint_edges += 1
+            continue
+        if source == target:
+            self_loop_edges += 1
+        valid_candidate_edges += 1
+        directed_pair = (source, target)
+        undirected_pair = (source, target) if source <= target else (target, source)
+        directed_pairs[directed_pair] += 1
+        undirected_pairs[undirected_pair] += 1
+        grouped[directed_pair].append(edge)
+
+    examples: list[dict[str, Any]] = []
+    if max_examples > 0:
+        for (source, target), count in directed_pairs.most_common():
+            if count < 2:
+                continue
+            edges = grouped[(source, target)]
+            examples.append(
+                {
+                    "source": source,
+                    "target": target,
+                    "edge_count": count,
+                    "relations": sorted({edge["relation"] for edge in edges}),
+                    "source_files": sorted({edge["source_file"] for edge in edges}),
+                    "source_locations": sorted({edge["source_location"] for edge in edges}),
+                    "contexts": sorted({edge["context"] for edge in edges}),
+                }
+            )
+            if len(examples) >= max_examples:
+                break
+
+    build_error = ""
+    graph_type = ""
+    post_build_edge_count: int | None = None
+    post_build_node_count: int | None = None
+    try:
+        graph_input = deepcopy(extraction)
+        graph: nx.Graph = build_from_json(graph_input, directed=directed, root=root)
+        graph_type = type(graph).__name__
+        post_build_edge_count = graph.number_of_edges()
+        post_build_node_count = graph.number_of_nodes()
+    except Exception as exc:
+        build_error = f"{type(exc).__name__}: {exc}"
+
+    suppression_path = (
+        Path(extract_path) if extract_path else Path(__file__).with_name("extract.py")
+    )
+
+    return {
+        "node_count": len(node_ids),
+        "raw_edge_count": len(raw_edges),
+        "non_object_edges": non_object_edges,
+        "missing_endpoint_edges": missing_endpoint_edges,
+        "dangling_endpoint_edges": dangling_endpoint_edges,
+        "self_loop_edges": self_loop_edges,
+        "valid_candidate_edges": valid_candidate_edges,
+        "exact_duplicate_edges": _count_extra(exact_counts),
+        "directed_unique_endpoint_pairs": len(directed_pairs),
+        "directed_same_endpoint_collapsed_edges": _count_extra(directed_pairs),
+        "undirected_unique_endpoint_pairs": len(undirected_pairs),
+        "undirected_same_endpoint_collapsed_edges": _count_extra(undirected_pairs),
+        "same_endpoint_group_count": sum(1 for count in directed_pairs.values() if count > 1),
+        "relation_variant_groups": _variant_group_count(grouped, "relation"),
+        "source_file_variant_groups": _variant_group_count(
+            grouped, "source_file", relation_sensitive=True
+        ),
+        "source_location_variant_groups": _variant_group_count(
+            grouped, "source_location", relation_sensitive=True
+        ),
+        "context_variant_groups": _variant_group_count(grouped, "context", relation_sensitive=True),
+        "post_build_graph_type": graph_type,
+        "post_build_node_count": post_build_node_count,
+        "post_build_edge_count": post_build_edge_count,
+        "post_build_error": build_error,
+        "producer_suppression": scan_producer_suppression_sites(suppression_path),
+        "examples": examples,
+    }
+
+
+def _read_json_file(path: str | Path) -> dict[str, Any]:
+    """Read a JSON graph after applying Graphify's graph-load size cap."""
+    from graphify.security import check_graph_file_size_cap
+
+    json_path = Path(path)
+    check_graph_file_size_cap(json_path)
+    data = json.loads(json_path.read_text(encoding="utf-8"))
+    if not isinstance(data, dict):
+        raise ValueError("diagnostic input must be a JSON object")
+    return data
+
+
+def diagnose_file(
+    path: str | Path,
+    *,
+    directed: bool | None = None,
+    root: str | Path | None = None,
+    max_examples: int = 5,
+    extract_path: str | Path | None = None,
+) -> dict[str, Any]:
+    """Diagnose a graph/extraction JSON file without mutating it.
+
+    When `directed` is None, the JSON's "directed" flag is honored. Raw
+    extraction JSON that has no "directed" flag defaults to directed analysis.
+    """
+    data = _read_json_file(path)
+    if directed is None:
+        raw_directed = data.get("directed")
+        effective_directed = raw_directed if isinstance(raw_directed, bool) else True
+    else:
+        effective_directed = directed
+
+    summary = diagnose_extraction(
+        data,
+        directed=effective_directed,
+        root=root,
+        max_examples=max_examples,
+        extract_path=extract_path,
+    )
+    summary["input_path"] = str(path)
+    summary["effective_directed"] = effective_directed
+    return summary
+
+
+def format_diagnostic_json(summary: dict[str, Any]) -> dict[str, Any]:
+    return {
+        "schema_version": 1,
+        "summary": {
+            key: value
+            for key, value in summary.items()
+            if key not in {"examples", "producer_suppression"}
+        },
+        "examples": summary.get("examples", []),
+        "producer_suppression": summary.get("producer_suppression", {}),
+        "notes": [
+            "Diagnostics are read-only.",
+            "A normal graph.json is already post-build and cannot recover raw producer edges.",
+            "Producer suppression sites are heuristic source-code evidence.",
+        ],
+    }
+
+
+def format_diagnostic_report(summary: dict[str, Any]) -> str:
+    suppression = summary.get("producer_suppression", {})
+    lines = [
+        "[graphify] MultiDiGraph edge-collapse diagnostic",
+        f"input: {summary.get('input_path', '<in-memory>')}",
+        "input_stage: provided JSON (normal graph.json is post-build)",
+        f"effective_directed: {summary.get('effective_directed', '<direct-call>')}",
+        f"nodes: {summary['node_count']}",
+        f"raw_edges: {summary['raw_edge_count']}",
+        f"valid_candidate_edges: {summary['valid_candidate_edges']}",
+        f"missing_endpoint_edges: {summary['missing_endpoint_edges']}",
+        f"dangling_endpoint_edges: {summary['dangling_endpoint_edges']}",
+        f"self_loop_edges: {summary['self_loop_edges']}",
+        f"exact_duplicate_edges: {summary['exact_duplicate_edges']}",
+        f"directed_unique_endpoint_pairs: {summary['directed_unique_endpoint_pairs']}",
+        (
+            "directed_same_endpoint_collapsed_edges: "
+            f"{summary['directed_same_endpoint_collapsed_edges']}"
+        ),
+        f"undirected_unique_endpoint_pairs: {summary['undirected_unique_endpoint_pairs']}",
+        (
+            "undirected_same_endpoint_collapsed_edges: "
+            f"{summary['undirected_same_endpoint_collapsed_edges']}"
+        ),
+        f"same_endpoint_group_count: {summary['same_endpoint_group_count']}",
+        f"relation_variant_groups: {summary['relation_variant_groups']}",
+        f"source_file_variant_groups: {summary['source_file_variant_groups']}",
+        f"source_location_variant_groups: {summary['source_location_variant_groups']}",
+        f"context_variant_groups: {summary['context_variant_groups']}",
+        f"post_build_graph_type: {summary['post_build_graph_type']}",
+        f"post_build_edges: {summary['post_build_edge_count']}",
+        f"producer_suppression_sites: {suppression.get('total_sites', 0)}",
+    ]
+    if summary.get("post_build_error"):
+        lines.append(f"post_build_error: {summary['post_build_error']}")
+    if suppression.get("error"):
+        lines.append(f"producer_suppression_error: {suppression['error']}")
+    if suppression.get("sites"):
+        lines.append("producer_suppression_examples:")
+        for site in suppression["sites"][:8]:
+            lines.append(
+                f"  - L{site['line']} {site['name']} arity={site['tuple_arity'] or 'unknown'}"
+            )
+    if summary.get("examples"):
+        lines.append("examples:")
+        for example in summary["examples"]:
+            lines.append(
+                "  - "
+                f"{example['source']} -> {example['target']} "
+                f"edges={example['edge_count']} "
+                f"relations={example['relations']} "
+                f"locations={example['source_locations']} "
+                f"contexts={example['contexts']}"
+            )
+    lines.append(
+        "note: normal graph.json is post-build; raw producer loss must be measured earlier."
+    )
+    return "\n".join(lines)