fix(build): deduplicate spec-conformant method nodes and aliases (#3705)

(cherry picked from commit fefdb5f074)

graphify/build.py

@@ -1069,6 +1069,7 @@ def build_from_json(extraction: dict, *, directed: bool = False, root: str | Pat
     _loc_collisions: set[tuple[str, str]] = set()  # keys shared by 2+ AST nodes
     _noloc_nodes: dict[tuple[str, str], str] = {}  # (source_file, label) -> ghost node id
     _ast_file_nodes: list[tuple[str, str]] = []  # (node_id, source_file) for AST file-self nodes (#3344)
+    _ast_method_nodes: dict[tuple[str, str], list[str]] = {}  # (source_file, norm_method) -> [ast_nid, ...]
 
     # Pass 1: collect canonical nodes — AST-origin nodes take precedence over LLM nodes.
     # When 2+ AST nodes share a key (same-named symbols in same-named files across
@@ -1125,6 +1126,9 @@ def build_from_json(extraction: dict, *, directed: bool = False, root: str | Pat
                 # Pass 2b below can catch these by label alone.
                 if _is_file_node_label(label, sf):
                     _ast_file_nodes.append((nid, sf))
+                if label.startswith("."):
+                    m_name = label.removeprefix(".").removesuffix("()")
+                    _ast_method_nodes.setdefault((sf, m_name), []).append(nid)
             else:
                 # First non-AST node for this (file, label) wins as canonical; a
                 # later same-key node is a genuine same-file duplicate and still
@@ -1132,6 +1136,7 @@ def build_from_json(extraction: dict, *, directed: bool = False, root: str | Pat
                 _loc_nodes.setdefault(key, nid)
 
     # Pass 2: find ghosts — non-AST nodes that have an AST canonical twin.
+    _ghost_remap: dict[str, str] = {}  # ghost_id -> canonical_id
     for nid in sorted(node_set):
         attrs = G.nodes[nid]
         if attrs.get("_origin") == "ast":
@@ -1145,8 +1150,13 @@ def build_from_json(extraction: dict, *, directed: bool = False, root: str | Pat
             continue  # ambiguous key: no safe canonical winner, leave ghost intact
         if key in _loc_nodes and _loc_nodes[key] != nid:
             _noloc_nodes[key] = nid
+        elif key not in _loc_nodes:
+            # Spec-conformant method ghost omitting class segment / leading dot (#3705)
+            m_name = label.removeprefix(".").removesuffix("()")
+            m_candidates = _ast_method_nodes.get((sf, m_name), [])
+            if len(m_candidates) == 1:
+                _ghost_remap[nid] = m_candidates[0]
     # For every ghost that has an AST counterpart, record a remap.
-    _ghost_remap: dict[str, str] = {}  # ghost_id -> canonical_id
     for key, sem_id in _noloc_nodes.items():
         ast_id = _loc_nodes.get(key)
         if ast_id is not None:
@@ -1247,6 +1257,12 @@ def build_from_json(extraction: dict, *, directed: bool = False, root: str | Pat
             alias = old_stem + suffix
             _alias_candidates.setdefault(_normalize_id(alias), set()).add(nid)
             _alias_candidates.setdefault(alias, set()).add(nid)
+        if attrs.get("_origin") == "ast" and str(attrs.get("label", "")).startswith("."):
+            m_name = make_id(str(attrs.get("label", "")).strip().removeprefix(".").removesuffix("()"))
+            m_alias = f"{new_stem}_{m_name}"
+            if _normalize_id(nid) != _normalize_id(m_alias):
+                _alias_candidates.setdefault(_normalize_id(m_alias), set()).add(nid)
+                _alias_candidates.setdefault(m_alias, set()).add(nid)
     for alias_key, candidates in _alias_candidates.items():
         if len(candidates) == 1:
             norm_to_id.setdefault(alias_key, next(iter(candidates)))

tests/test_build.py

@@ -2001,3 +2001,50 @@ def test_build_annotations_all_resolve():
             except NameError as exc:
                 unresolvable.append(f"{name}: {exc}")
     assert not unresolvable, "\n".join(unresolvable)
+
+
+def test_method_ghost_dedupe_and_alias_resolution_3705():
+    from graphify.build import build_from_json
+
+    extraction = {
+        "nodes": [
+            # AST node with class segment and leading dot
+            {
+                "id": "broker_mock_tda_mocktdaaccount_save_state",
+                "label": ".save_state()",
+                "file_type": "code",
+                "source_file": "broker/mock_tda.py",
+                "source_location": "L220",
+                "_origin": "ast",
+            },
+            # Spec-conformant semantic ghost node (no class segment, no leading dot)
+            {
+                "id": "broker_mock_tda_save_state",
+                "label": "save_state()",
+                "file_type": "code",
+                "source_file": "broker/mock_tda.py",
+            },
+            {
+                "id": "doc_summary",
+                "label": "Doc Summary",
+                "file_type": "document",
+                "source_file": "docs/summary.md",
+            },
+        ],
+        "edges": [
+            {
+                "source": "doc_summary",
+                "target": "broker_mock_tda_save_state",
+                "relation": "references",
+                "confidence": "INFERRED",
+                "confidence_score": 0.85,
+                "source_file": "docs/summary.md",
+            }
+        ],
+    }
+    G = build_from_json(extraction)
+    # The ghost node should be removed/remapped into the canonical AST node
+    assert "broker_mock_tda_save_state" not in G.nodes
+    assert "broker_mock_tda_mocktdaaccount_save_state" in G.nodes
+    assert G.has_edge("doc_summary", "broker_mock_tda_mocktdaaccount_save_state")
+