codegraphcontext-rust 0.5.5__cp310-cp310-win_amd64.whl

codegraphcontext/tools/indexing/persistence/writer.py

@@ -0,0 +1,1114 @@
+"""All graph DB writes for indexing (single persistence entry point)."""
+
+from __future__ import annotations
+
+import time
+from pathlib import Path
+from typing import Any, Callable, Dict, List, Optional, Tuple
+
+from ....utils.debug_log import info_logger, warning_logger
+from ..sanitize import sanitize_props
+
+
+class GraphWriter:
+    """Persists repository/file/symbol nodes and relationships via the Neo4j-like driver API."""
+
+    def __init__(self, driver: Any):
+        self.driver = driver
+
+    def add_repository_to_graph(self, repo_path: Path, is_dependency: bool = False) -> None:
+        repo_name = repo_path.name
+        repo_path_str = str(repo_path.resolve())
+        with self.driver.session() as session:
+            session.run(
+                """
+                MERGE (r:Repository {path: $path})
+                SET r.name = $name, r.is_dependency = $is_dependency
+                """,
+                path=repo_path_str,
+                name=repo_name,
+                is_dependency=is_dependency,
+            )
+
+    def add_file_to_graph(
+        self,
+        file_data: Dict[str, Any],
+        repo_name: str,
+        imports_map: dict,
+        repo_path_str: Optional[str] = None,
+    ) -> None:
+        file_path_str = str(Path(file_data["path"]).resolve())
+        file_name = Path(file_path_str).name
+        is_dependency = file_data.get("is_dependency", False)
+        lang = file_data.get("lang")
+
+        with self.driver.session() as session:
+            if repo_path_str:
+                resolved_repo_str = repo_path_str
+            else:
+                repo_result = session.run(
+                    "MATCH (r:Repository {path: $repo_path}) RETURN r.path as path",
+                    repo_path=str(Path(file_data["repo_path"]).resolve()),
+                ).single()
+                resolved_repo_str = (
+                    repo_result["path"] if repo_result else str(Path(file_data["repo_path"]).resolve())
+                )
+                if not repo_result:
+                    warning_logger(
+                        f"Repository node not found for {file_data['repo_path']} during indexing of {file_name}."
+                    )
+
+            try:
+                relative_path = str(Path(file_path_str).relative_to(Path(resolved_repo_str)))
+            except ValueError:
+                relative_path = file_name
+
+            session.run(
+                """
+                MERGE (f:File {path: $path})
+                SET f.name = $name, f.relative_path = $relative_path, f.is_dependency = $is_dependency
+            """,
+                path=file_path_str,
+                name=file_name,
+                relative_path=relative_path,
+                is_dependency=is_dependency,
+            )
+
+            file_path_obj = Path(file_path_str)
+            repo_path_obj = Path(resolved_repo_str)
+            relative_path_to_file = file_path_obj.relative_to(repo_path_obj)
+            parent_path = resolved_repo_str
+            parent_label = "Repository"
+            for part in relative_path_to_file.parts[:-1]:
+                current_path_str = str(Path(parent_path) / part)
+                session.run(
+                    f"""
+                    MATCH (p:{parent_label} {{path: $parent_path}})
+                    MERGE (d:Directory {{path: $current_path}})
+                    SET d.name = $part
+                    MERGE (p)-[:CONTAINS]->(d)
+                """,
+                    parent_path=parent_path,
+                    current_path=current_path_str,
+                    part=part,
+                )
+                parent_path = current_path_str
+                parent_label = "Directory"
+            session.run(
+                f"""
+                MATCH (p:{parent_label} {{path: $parent_path}})
+                MATCH (f:File {{path: $path}})
+                MERGE (p)-[:CONTAINS]->(f)
+            """,
+                parent_path=parent_path,
+                path=file_path_str,
+            )
+
+            item_mappings = [
+                (file_data.get("functions", []), "Function"),
+                (file_data.get("classes", []), "Class"),
+                (file_data.get("traits", []), "Trait"),
+                (file_data.get("variables", []), "Variable"),
+                (file_data.get("interfaces", []), "Interface"),
+                (file_data.get("macros", []), "Macro"),
+                (file_data.get("structs", []), "Struct"),
+                (file_data.get("enums", []), "Enum"),
+                (file_data.get("unions", []), "Union"),
+                (file_data.get("records", []), "Record"),
+                (file_data.get("properties", []), "Property"),
+            ]
+            params_batch: List[Dict[str, Any]] = []
+            class_fn_batch: List[Dict[str, Any]] = []
+            nested_fn_batch: List[Dict[str, Any]] = []
+
+            for item_list, label in item_mappings:
+                if not item_list:
+                    continue
+                batch: List[Dict[str, Any]] = []
+                for item in item_list:
+                    row = dict(item)
+                    if label == "Function" and "cyclomatic_complexity" not in row:
+                        row["cyclomatic_complexity"] = 1
+                    batch.append(sanitize_props(row))
+                    if label == "Function":
+                        for arg_name in item.get("args", []):
+                            params_batch.append(
+                                {
+                                    "func_name": item["name"],
+                                    "line_number": item["line_number"],
+                                    "arg_name": arg_name,
+                                }
+                            )
+                        if item.get("class_context"):
+                            class_fn_batch.append(
+                                {
+                                    "class_name": item["class_context"],
+                                    "func_name": item["name"],
+                                    "func_line": item["line_number"],
+                                }
+                            )
+                        if item.get("context_type") == "function_definition":
+                            nested_fn_batch.append(
+                                {
+                                    "outer": item["context"],
+                                    "inner_name": item["name"],
+                                    "inner_line": item["line_number"],
+                                }
+                            )
+
+                if batch:
+                    import json as _json
+
+                    all_keys = set()
+                    for b in batch:
+                        all_keys.update(b.keys())
+
+                    for k in all_keys:
+                        counts: Dict[str, int] = {}
+                        for b in batch:
+                            v = b.get(k)
+                            if v is not None:
+                                tname = type(v).__name__
+                                counts[tname] = counts.get(tname, 0) + 1
+
+                        dominant = max(counts, key=counts.get) if counts else "str"
+
+                        for b in batch:
+                            v = b.get(k)
+                            if dominant == "list":
+                                if isinstance(v, list):
+                                    b[k] = [str(x) for x in v] if v else [""]
+                                elif isinstance(v, str) and v:
+                                    try:
+                                        p = _json.loads(v)
+                                        b[k] = [str(x) for x in p] if isinstance(p, list) and p else [""]
+                                    except Exception:
+                                        b[k] = [v]
+                                else:
+                                    b[k] = [""]
+                            elif dominant == "int":
+                                if v is None or v == "":
+                                    b[k] = 0
+                                elif not isinstance(v, int):
+                                    try:
+                                        b[k] = int(v)
+                                    except Exception:
+                                        b[k] = 0
+                            elif dominant == "bool":
+                                b[k] = bool(v) if v is not None else False
+                            else:
+                                if v is None:
+                                    b[k] = ""
+                                elif isinstance(v, list):
+                                    b[k] = _json.dumps(v)
+                                elif not isinstance(v, str):
+                                    b[k] = str(v)
+
+                    key_order = sorted(all_keys)
+                    batch[:] = [{k: b[k] for k in key_order} for b in batch]
+
+                session.run(
+                    f"""
+                    UNWIND $batch AS row
+                    MERGE (n:{label} {{name: row.name, path: $file_path, line_number: row.line_number}})
+                    SET n += row
+                """,
+                    batch=batch,
+                    file_path=file_path_str,
+                )
+                session.run(
+                    f"""
+                    UNWIND $batch AS row
+                    MATCH (f:File {{path: $file_path}})
+                    MATCH (n:{label} {{name: row.name, path: $file_path, line_number: row.line_number}})
+                    MERGE (f)-[:CONTAINS]->(n)
+                """,
+                    batch=batch,
+                    file_path=file_path_str,
+                )
+
+            if params_batch:
+                session.run(
+                    """
+                    UNWIND $batch AS row
+                    MATCH (fn:Function {name: row.func_name, path: $file_path, line_number: row.line_number})
+                    MERGE (p:Parameter {name: row.arg_name, path: $file_path, function_line_number: row.line_number})
+                    MERGE (fn)-[:HAS_PARAMETER]->(p)
+                """,
+                    batch=params_batch,
+                    file_path=file_path_str,
+                )
+
+            if class_fn_batch:
+                session.run(
+                    """
+                    UNWIND $batch AS row
+                    MATCH (c:Class {name: row.class_name, path: $file_path})
+                    MATCH (fn:Function {name: row.func_name, path: $file_path, line_number: row.func_line})
+                    MERGE (c)-[:CONTAINS]->(fn)
+                """,
+                    batch=class_fn_batch,
+                    file_path=file_path_str,
+                )
+
+            if nested_fn_batch:
+                session.run(
+                    """
+                    UNWIND $batch AS row
+                    MATCH (outer:Function {name: row.outer, path: $file_path})
+                    MATCH (inner:Function {name: row.inner_name, path: $file_path, line_number: row.inner_line})
+                    MERGE (outer)-[:CONTAINS]->(inner)
+                """,
+                    batch=nested_fn_batch,
+                    file_path=file_path_str,
+                )
+
+            ruby_modules = file_data.get("modules", [])
+            if ruby_modules:
+                session.run(
+                    """
+                    UNWIND $batch AS row
+                    MERGE (mod:Module {name: row.name})
+                    ON CREATE SET mod.lang = row.lang
+                    ON MATCH  SET mod.lang = coalesce(mod.lang, row.lang)
+                """,
+                    batch=[{"name": m["name"], "lang": lang} for m in ruby_modules],
+                )
+
+            js_imports = []
+            other_imports = []
+            for imp in file_data.get("imports", []):
+                if lang == "javascript":
+                    module_name = imp.get("source")
+                    if module_name:
+                        js_imports.append(
+                            {
+                                "module_name": module_name,
+                                "imported_name": imp.get("name", "*"),
+                                "alias": imp.get("alias"),
+                                "line_number": imp.get("line_number"),
+                            }
+                        )
+                else:
+                    other_imports.append(imp)
+
+            if js_imports:
+                session.run(
+                    """
+                    UNWIND $batch AS row
+                    MATCH (f:File {path: $file_path})
+                    MERGE (m:Module {name: row.module_name})
+                    MERGE (f)-[r:IMPORTS]->(m)
+                    SET r.imported_name = row.imported_name,
+                        r.alias = row.alias,
+                        r.line_number = row.line_number
+                """,
+                    batch=js_imports,
+                    file_path=file_path_str,
+                )
+
+            if other_imports:
+                session.run(
+                    """
+                    UNWIND $batch AS row
+                    MATCH (f:File {path: $file_path})
+                    MERGE (m:Module {name: row.name})
+                    SET m.alias = row.alias,
+                        m.full_import_name = coalesce(row.full_import_name, m.full_import_name)
+                    MERGE (f)-[r:IMPORTS]->(m)
+                    SET r.line_number = row.line_number,
+                        r.alias = row.alias
+                """,
+                    batch=other_imports,
+                    file_path=file_path_str,
+                )
+
+            module_inclusions = file_data.get("module_inclusions", [])
+            if module_inclusions:
+                session.run(
+                    """
+                    UNWIND $batch AS row
+                    MATCH (c:Class {name: row.class_name, path: $file_path})
+                    MERGE (m:Module {name: row.module_name})
+                    MERGE (c)-[:INCLUDES]->(m)
+                """,
+                    batch=[
+                        {"class_name": i["class"], "module_name": i["module"]} for i in module_inclusions
+                    ],
+                    file_path=file_path_str,
+                )
+
+    # ── Batch write (10-20x faster than per-file add_file_to_graph) ──────────
+
+    def add_files_batch_to_graph(
+        self,
+        all_file_data: List[Dict[str, Any]],
+        repo_name: str,
+        imports_map: dict,
+        repo_path_str: str,
+        on_progress: Optional[Callable] = None,
+    ) -> int:
+        """Write all parsed files to graph in batched queries.
+
+        Instead of N×12 individual queries, this runs ~12 batched UNWIND
+        queries total, reducing KuzuDB transaction overhead dramatically.
+
+        Returns the number of files successfully written.
+        """
+        import json as _json
+
+        repo_path_obj = Path(repo_path_str)
+        total = len(all_file_data)
+
+        # ── Collect all data into flat batches ──────────────────────────
+        file_batch = []
+        dir_batch = []          # (parent_path, parent_label, dir_path, dir_name)
+        file_parent_batch = []  # (parent_path, parent_label, file_path)
+        symbol_batches: Dict[str, List[Dict]] = {}  # label → [rows]
+        symbol_file_batches: Dict[str, List[Dict]] = {}  # label → [(file_path, name, line)]
+        params_batch = []
+        class_fn_batch = []
+        nested_fn_batch = []
+        js_imports_batch = []
+        other_imports_batch = []
+
+        for idx, file_data in enumerate(all_file_data):
+            file_path_str = str(Path(file_data["path"]).resolve())
+            file_name = Path(file_path_str).name
+            is_dep = file_data.get("is_dependency", False)
+            lang = file_data.get("lang")
+
+            try:
+                rel_path = str(Path(file_path_str).relative_to(repo_path_obj))
+            except ValueError:
+                rel_path = file_name
+
+            file_batch.append({
+                "path": file_path_str, "name": file_name,
+                "relative_path": rel_path, "is_dependency": is_dep,
+            })
+
+            # Directory chain
+            try:
+                rel_to_file = Path(file_path_str).relative_to(repo_path_obj)
+            except ValueError:
+                rel_to_file = Path(file_name)
+
+            parent_path = repo_path_str
+            parent_label = "Repository"
+            for part in rel_to_file.parts[:-1]:
+                cur = str(Path(parent_path) / part)
+                dir_batch.append({
+                    "parent_path": parent_path, "parent_label": parent_label,
+                    "dir_path": cur, "dir_name": part,
+                })
+                parent_path = cur
+                parent_label = "Directory"
+            file_parent_batch.append({
+                "parent_path": parent_path, "parent_label": parent_label,
+                "file_path": file_path_str,
+            })
+
+            # Symbols
+            item_mappings = [
+                (file_data.get("functions", []), "Function"),
+                (file_data.get("classes", []), "Class"),
+                (file_data.get("traits", []), "Trait"),
+                (file_data.get("variables", []), "Variable"),
+                (file_data.get("interfaces", []), "Interface"),
+                (file_data.get("macros", []), "Macro"),
+                (file_data.get("structs", []), "Struct"),
+                (file_data.get("enums", []), "Enum"),
+                (file_data.get("unions", []), "Union"),
+                (file_data.get("records", []), "Record"),
+                (file_data.get("properties", []), "Property"),
+            ]
+
+            for item_list, label in item_mappings:
+                if not item_list:
+                    continue
+                if label not in symbol_batches:
+                    symbol_batches[label] = []
+                    symbol_file_batches[label] = []
+                for item in item_list:
+                    row = dict(item)
+                    row["_file_path"] = file_path_str
+                    if label == "Function" and "cyclomatic_complexity" not in row:
+                        row["cyclomatic_complexity"] = 1
+                    symbol_batches[label].append(sanitize_props(row))
+                    symbol_file_batches[label].append({
+                        "file_path": file_path_str,
+                        "name": item["name"],
+                        "line_number": item["line_number"],
+                    })
+
+                    if label == "Function":
+                        for arg_name in item.get("args", []):
+                            params_batch.append({
+                                "func_name": item["name"],
+                                "line_number": item["line_number"],
+                                "arg_name": arg_name,
+                                "file_path": file_path_str,
+                            })
+                        if item.get("class_context"):
+                            class_fn_batch.append({
+                                "class_name": item["class_context"],
+                                "func_name": item["name"],
+                                "func_line": item["line_number"],
+                                "file_path": file_path_str,
+                            })
+                        if item.get("context_type") == "function_definition":
+                            nested_fn_batch.append({
+                                "outer": item["context"],
+                                "inner_name": item["name"],
+                                "inner_line": item["line_number"],
+                                "file_path": file_path_str,
+                            })
+
+            # Imports
+            for imp in file_data.get("imports", []):
+                if lang == "javascript":
+                    module_name = imp.get("source")
+                    if module_name:
+                        js_imports_batch.append({
+                            "module_name": module_name,
+                            "imported_name": imp.get("name", "*"),
+                            "alias": imp.get("alias"),
+                            "line_number": imp.get("line_number"),
+                            "file_path": file_path_str,
+                        })
+                else:
+                    other_imports_batch.append({
+                        "name": imp.get("name", ""),
+                        "alias": imp.get("alias"),
+                        "full_import_name": imp.get("full_import_name", imp.get("name", "")),
+                        "line_number": imp.get("line_number"),
+                        "file_path": file_path_str,
+                    })
+
+        # ── Execute batched queries ─────────────────────────────────────
+        if on_progress:
+            on_progress(0, total, "Writing files to graph...")
+
+        batch_size = 500
+
+        with self.driver.session() as session:
+            # 1. Files
+            for i in range(0, len(file_batch), batch_size):
+                session.run(
+                    "UNWIND $batch AS row "
+                    "MERGE (f:File {path: row.path}) "
+                    "SET f.name = row.name, f.relative_path = row.relative_path, "
+                    "    f.is_dependency = row.is_dependency",
+                    batch=file_batch[i:i + batch_size],
+                )
+
+            if on_progress:
+                on_progress(total // 4, total, "Writing directories...")
+
+            # 2. Directories (grouped by parent_label to avoid dynamic labels)
+            for plabel in ("Repository", "Directory"):
+                subset = [d for d in dir_batch if d["parent_label"] == plabel]
+                for i in range(0, len(subset), batch_size):
+                    chunk = [{k: v for k, v in d.items() if k != "parent_label"} for d in subset[i:i + batch_size]]
+                    session.run(
+                        f"UNWIND $batch AS row "
+                        f"MATCH (p:{plabel} {{path: row.parent_path}}) "
+                        f"MERGE (d:Directory {{path: row.dir_path}}) "
+                        f"SET d.name = row.dir_name "
+                        f"MERGE (p)-[:CONTAINS]->(d)",
+                        batch=chunk,
+                    )
+
+            # 3. File-parent CONTAINS
+            for plabel in ("Repository", "Directory"):
+                subset = [d for d in file_parent_batch if d["parent_label"] == plabel]
+                for i in range(0, len(subset), batch_size):
+                    chunk = [{k: v for k, v in d.items() if k != "parent_label"} for d in subset[i:i + batch_size]]
+                    session.run(
+                        f"UNWIND $batch AS row "
+                        f"MATCH (p:{plabel} {{path: row.parent_path}}) "
+                        f"MATCH (f:File {{path: row.file_path}}) "
+                        f"MERGE (p)-[:CONTAINS]->(f)",
+                        batch=chunk,
+                    )
+
+            if on_progress:
+                on_progress(total // 2, total, "Writing symbols...")
+
+            # 4. Symbols (per label)
+            for label, batch in symbol_batches.items():
+                # Normalize types across batch
+                all_keys = set()
+                for b in batch:
+                    all_keys.update(b.keys())
+                all_keys.discard("_file_path")
+
+                for k in all_keys:
+                    counts: Dict[str, int] = {}
+                    for b in batch:
+                        v = b.get(k)
+                        if v is not None:
+                            tname = type(v).__name__
+                            counts[tname] = counts.get(tname, 0) + 1
+                    dominant = max(counts, key=counts.get) if counts else "str"
+
+                    for b in batch:
+                        v = b.get(k)
+                        if dominant == "list":
+                            if isinstance(v, list):
+                                b[k] = [str(x) for x in v] if v else [""]
+                            elif isinstance(v, str) and v:
+                                try:
+                                    p = _json.loads(v)
+                                    b[k] = [str(x) for x in p] if isinstance(p, list) and p else [""]
+                                except Exception:
+                                    b[k] = [v]
+                            else:
+                                b[k] = [""]
+                        elif dominant == "int":
+                            if v is None or v == "":
+                                b[k] = 0
+                            elif not isinstance(v, int):
+                                try:
+                                    b[k] = int(v)
+                                except Exception:
+                                    b[k] = 0
+                        elif dominant == "bool":
+                            b[k] = bool(v) if v is not None else False
+                        else:
+                            if v is None:
+                                b[k] = ""
+                            elif isinstance(v, list):
+                                b[k] = _json.dumps(v)
+                            elif not isinstance(v, str):
+                                b[k] = str(v)
+
+                key_order = sorted(all_keys)
+                normalized = []
+                file_paths_for_batch = []
+                for b in batch:
+                    fp = b.pop("_file_path", "")
+                    normalized.append({k: b[k] for k in key_order if k in b})
+                    file_paths_for_batch.append(fp)
+
+                # Deduplicate by (name, path, line_number) — minified JS can
+                # produce duplicates which violate KuzuDB primary key constraint
+                seen_keys = set()
+                deduped = []
+                deduped_fps = []
+                for row, fp in zip(normalized, file_paths_for_batch):
+                    key = (row.get("name", ""), fp, row.get("line_number", 0))
+                    if key not in seen_keys:
+                        seen_keys.add(key)
+                        deduped.append(row)
+                        deduped_fps.append(fp)
+                normalized = deduped
+                file_paths_for_batch = deduped_fps
+
+                # Write symbols in chunks
+                for i in range(0, len(normalized), batch_size):
+                    chunk = normalized[i:i + batch_size]
+                    fps = file_paths_for_batch[i:i + batch_size]
+                    # Add file_path back for MERGE key
+                    for row, fp in zip(chunk, fps):
+                        row["_fp"] = fp
+
+                    session.run(
+                        f"UNWIND $batch AS row "
+                        f"MERGE (n:{label} {{name: row.name, path: row._fp, line_number: row.line_number}}) "
+                        f"SET n += row",
+                        batch=chunk,
+                    )
+                    session.run(
+                        f"UNWIND $batch AS row "
+                        f"MATCH (f:File {{path: row._fp}}) "
+                        f"MATCH (n:{label} {{name: row.name, path: row._fp, line_number: row.line_number}}) "
+                        f"MERGE (f)-[:CONTAINS]->(n)",
+                        batch=chunk,
+                    )
+
+            if on_progress:
+                on_progress(total * 3 // 4, total, "Writing relationships...")
+
+            # 5. Parameters
+            if params_batch:
+                for i in range(0, len(params_batch), batch_size):
+                    session.run(
+                        "UNWIND $batch AS row "
+                        "MATCH (fn:Function {name: row.func_name, path: row.file_path, line_number: row.line_number}) "
+                        "MERGE (p:Parameter {name: row.arg_name, path: row.file_path, function_line_number: row.line_number}) "
+                        "MERGE (fn)-[:HAS_PARAMETER]->(p)",
+                        batch=params_batch[i:i + batch_size],
+                    )
+
+            # 6. Class-function containment
+            if class_fn_batch:
+                for i in range(0, len(class_fn_batch), batch_size):
+                    session.run(
+                        "UNWIND $batch AS row "
+                        "MATCH (c:Class {name: row.class_name, path: row.file_path}) "
+                        "MATCH (fn:Function {name: row.func_name, path: row.file_path, line_number: row.func_line}) "
+                        "MERGE (c)-[:CONTAINS]->(fn)",
+                        batch=class_fn_batch[i:i + batch_size],
+                    )
+
+            # 7. Nested functions
+            if nested_fn_batch:
+                for i in range(0, len(nested_fn_batch), batch_size):
+                    session.run(
+                        "UNWIND $batch AS row "
+                        "MATCH (outer:Function {name: row.outer, path: row.file_path}) "
+                        "MATCH (inner:Function {name: row.inner_name, path: row.file_path, line_number: row.inner_line}) "
+                        "MERGE (outer)-[:CONTAINS]->(inner)",
+                        batch=nested_fn_batch[i:i + batch_size],
+                    )
+
+            # 8. JS imports
+            if js_imports_batch:
+                for i in range(0, len(js_imports_batch), batch_size):
+                    session.run(
+                        "UNWIND $batch AS row "
+                        "MATCH (f:File {path: row.file_path}) "
+                        "MERGE (m:Module {name: row.module_name}) "
+                        "MERGE (f)-[r:IMPORTS]->(m) "
+                        "SET r.imported_name = row.imported_name, r.alias = row.alias, r.line_number = row.line_number",
+                        batch=js_imports_batch[i:i + batch_size],
+                    )
+
+            # 9. Other imports
+            if other_imports_batch:
+                for i in range(0, len(other_imports_batch), batch_size):
+                    session.run(
+                        "UNWIND $batch AS row "
+                        "MATCH (f:File {path: row.file_path}) "
+                        "MERGE (m:Module {name: row.name}) "
+                        "SET m.alias = row.alias, m.full_import_name = coalesce(row.full_import_name, m.full_import_name) "
+                        "MERGE (f)-[r:IMPORTS]->(m) "
+                        "SET r.line_number = row.line_number, r.alias = row.alias",
+                        batch=other_imports_batch[i:i + batch_size],
+                    )
+
+        if on_progress:
+            on_progress(total, total, "Graph write complete")
+
+        return len(file_batch)
+
+    def add_minimal_file_node(
+        self, file_path: Path, repo_path: Path, is_dependency: bool = False
+    ) -> None:
+        file_path_str = str(file_path.resolve())
+        file_name = file_path.name
+        repo_name = repo_path.name
+        repo_path_str = str(repo_path.resolve())
+
+        with self.driver.session() as session:
+            session.run(
+                """
+                MERGE (r:Repository {path: $repo_path})
+                SET r.name = $repo_name
+                """,
+                repo_path=repo_path_str,
+                repo_name=repo_name,
+            )
+
+            session.run(
+                """
+                MERGE (f:File {path: $file_path})
+                SET f.name = $file_name,
+                    f.is_dependency = $is_dependency
+                """,
+                file_path=file_path_str,
+                file_name=file_name,
+                is_dependency=is_dependency,
+            )
+
+            file_path_obj = Path(file_path_str)
+            repo_path_obj = Path(repo_path_str)
+            try:
+                relative_path_to_file = file_path_obj.relative_to(repo_path_obj)
+            except ValueError:
+                relative_path_to_file = Path(file_path_obj.name)
+
+            parent_path = repo_path_str
+            parent_label = "Repository"
+
+            for part in relative_path_to_file.parts[:-1]:
+                current_path = Path(parent_path) / part
+                current_path_str = str(current_path)
+
+                session.run(
+                    f"""
+                    MATCH (p:{parent_label} {{path: $parent_path}})
+                    MERGE (d:Directory {{path: $current_path}})
+                    SET d.name = $part
+                    MERGE (p)-[:CONTAINS]->(d)
+                """,
+                    parent_path=parent_path,
+                    current_path=current_path_str,
+                    part=part,
+                )
+
+                parent_path = current_path_str
+                parent_label = "Directory"
+
+            session.run(
+                f"""
+                MATCH (p:{parent_label} {{path: $parent_path}})
+                MATCH (f:File {{path: $file_path}})
+                MERGE (p)-[:CONTAINS]->(f)
+            """,
+                parent_path=parent_path,
+                file_path=file_path_str,
+            )
+
+    def write_function_call_groups(
+        self,
+        fn_to_fn: List[Dict],
+        fn_to_cls: List[Dict],
+        cls_to_fn: List[Dict],
+        cls_to_cls: List[Dict],
+        file_to_fn: List[Dict],
+        file_to_cls: List[Dict],
+    ) -> None:
+        batch_size = 1000
+        q_fn_to_fn = """
+            UNWIND $batch AS row
+            MATCH (caller:Function {name: row.caller_name, path: row.caller_file_path, line_number: row.caller_line_number})
+            MATCH (called:Function {name: row.called_name, path: row.called_file_path})
+            MERGE (caller)-[:CALLS {line_number: row.line_number, args: row.args, full_call_name: row.full_call_name}]->(called)
+        """
+        q_fn_to_cls = """
+            UNWIND $batch AS row
+            MATCH (caller:Function {name: row.caller_name, path: row.caller_file_path, line_number: row.caller_line_number})
+            MATCH (called:Class {name: row.called_name, path: row.called_file_path})
+            MERGE (caller)-[:CALLS {line_number: row.line_number, args: row.args, full_call_name: row.full_call_name}]->(called)
+        """
+        q_cls_to_fn = """
+            UNWIND $batch AS row
+            MATCH (caller:Class {name: row.caller_name, path: row.caller_file_path, line_number: row.caller_line_number})
+            MATCH (called:Function {name: row.called_name, path: row.called_file_path})
+            MERGE (caller)-[:CALLS {line_number: row.line_number, args: row.args, full_call_name: row.full_call_name}]->(called)
+        """
+        q_cls_to_cls = """
+            UNWIND $batch AS row
+            MATCH (caller:Class {name: row.caller_name, path: row.caller_file_path, line_number: row.caller_line_number})
+            MATCH (called:Class {name: row.called_name, path: row.called_file_path})
+            MERGE (caller)-[:CALLS {line_number: row.line_number, args: row.args, full_call_name: row.full_call_name}]->(called)
+        """
+        q_file_to_fn = """
+            UNWIND $batch AS row
+            MATCH (caller:File {path: row.caller_file_path})
+            MATCH (called:Function {name: row.called_name, path: row.called_file_path})
+            MERGE (caller)-[:CALLS {line_number: row.line_number, args: row.args, full_call_name: row.full_call_name}]->(called)
+        """
+        q_file_to_cls = """
+            UNWIND $batch AS row
+            MATCH (caller:File {path: row.caller_file_path})
+            MATCH (called:Class {name: row.called_name, path: row.called_file_path})
+            MERGE (caller)-[:CALLS {line_number: row.line_number, args: row.args, full_call_name: row.full_call_name}]->(called)
+        """
+        groups: List[Tuple[str, List[Dict], str]] = [
+            ("fn→fn", fn_to_fn, q_fn_to_fn),
+            ("fn→cls", fn_to_cls, q_fn_to_cls),
+            ("cls→fn", cls_to_fn, q_cls_to_fn),
+            ("cls→cls", cls_to_cls, q_cls_to_cls),
+            ("file→fn", file_to_fn, q_file_to_fn),
+            ("file→cls", file_to_cls, q_file_to_cls),
+        ]
+        total_all = sum(len(g[1]) for g in groups)
+        with self.driver.session() as session:
+            for label, calls, query in groups:
+                if not calls:
+                    info_logger(f"[CALLS] {label}: 0 (skipped)")
+                    continue
+                t0 = time.time()
+                for i in range(0, len(calls), batch_size):
+                    batch = calls[i : i + batch_size]
+                    session.run(query, batch=batch)
+                    written = min(i + batch_size, len(calls))
+                    if written % 5000 < batch_size or written == len(calls):
+                        elapsed = time.time() - t0
+                        info_logger(f"[CALLS] {label}: {written}/{len(calls)} ({elapsed:.1f}s)")
+                elapsed = time.time() - t0
+                info_logger(f"[CALLS] {label} done: {len(calls)} in {elapsed:.1f}s")
+        info_logger(f"[CALLS] All complete: {total_all} CALLS relationships processed.")
+
+    def _create_csharp_inheritance_and_interfaces(
+        self, session: Any, file_data: Dict[str, Any], imports_map: dict
+    ) -> None:
+        if file_data.get("lang") != "c_sharp":
+            return
+
+        caller_file_path = str(Path(file_data["path"]).resolve())
+
+        for type_list_name, type_label in [
+            ("classes", "Class"),
+            ("structs", "Struct"),
+            ("records", "Record"),
+            ("interfaces", "Interface"),
+        ]:
+            for type_item in file_data.get(type_list_name, []):
+                if not type_item.get("bases"):
+                    continue
+
+                for base_str in type_item["bases"]:
+                    base_name = base_str.split("<")[0].strip()
+
+                    is_interface = False
+                    resolved_path = caller_file_path
+
+                    for iface in file_data.get("interfaces", []):
+                        if iface["name"] == base_name:
+                            is_interface = True
+                            break
+
+                    if base_name in imports_map:
+                        possible_paths = imports_map[base_name]
+                        if len(possible_paths) > 0:
+                            resolved_path = possible_paths[0]
+
+                    base_index = type_item["bases"].index(base_str)
+
+                    if is_interface or (base_index > 0 and type_label == "Class"):
+                        session.run(
+                            """
+                            MATCH (child {name: $child_name, path: $path})
+                            WHERE child:Class OR child:Struct OR child:Record
+                            MATCH (iface:Interface {name: $interface_name})
+                            MERGE (child)-[:IMPLEMENTS]->(iface)
+                        """,
+                            child_name=type_item["name"],
+                            path=caller_file_path,
+                            interface_name=base_name,
+                        )
+                    else:
+                        session.run(
+                            """
+                            MATCH (child {name: $child_name, path: $path})
+                            WHERE child:Class OR child:Record OR child:Interface
+                            MATCH (parent {name: $parent_name})
+                            WHERE parent:Class OR parent:Record OR parent:Interface
+                            MERGE (child)-[:INHERITS]->(parent)
+                        """,
+                            child_name=type_item["name"],
+                            path=caller_file_path,
+                            parent_name=base_name,
+                        )
+
+    def write_inheritance_links(
+        self,
+        inheritance_batch: List[Dict[str, Any]],
+        csharp_files: List[Dict[str, Any]],
+        imports_map: dict,
+    ) -> None:
+        info_logger(
+            f"[INHERITS] Resolved {len(inheritance_batch)} inheritance links, "
+            f"{len(csharp_files)} C# files. Writing to Neo4j..."
+        )
+        batch_size = 500
+        with self.driver.session() as session:
+            for i in range(0, len(inheritance_batch), batch_size):
+                batch = inheritance_batch[i : i + batch_size]
+                session.run(
+                    """
+                    UNWIND $batch AS row
+                    MATCH (child:Class {name: row.child_name, path: row.path})
+                    MATCH (parent:Class {name: row.parent_name, path: row.resolved_parent_file_path})
+                    MERGE (child)-[:INHERITS]->(parent)
+                """,
+                    batch=batch,
+                )
+
+            for file_data in csharp_files:
+                self._create_csharp_inheritance_and_interfaces(session, file_data, imports_map)
+
+        info_logger(f"[INHERITS] Complete: {len(inheritance_batch)} inheritance links processed.")
+
+    def write_scip_call_edges(
+        self, files_data: Dict[str, Any], name_from_symbol: Callable[[str], str]
+    ) -> None:
+        with self.driver.session() as session:
+            for file_data in files_data.values():
+                for edge in file_data.get("function_calls_scip", []):
+                    try:
+                        session.run(
+                            """
+                            MATCH (caller:Function {name: $caller_name, path: $caller_file, line_number: $caller_line})
+                            MATCH (callee:Function {name: $callee_name, path: $callee_file, line_number: $callee_line})
+                            MERGE (caller)-[:CALLS {line_number: $ref_line, source: 'scip'}]->(callee)
+                        """,
+                            caller_name=name_from_symbol(edge["caller_symbol"]),
+                            caller_file=edge["caller_file"],
+                            caller_line=edge["caller_line"],
+                            callee_name=edge["callee_name"],
+                            callee_file=edge["callee_file"],
+                            callee_line=edge["callee_line"],
+                            ref_line=edge["ref_line"],
+                        )
+                    except Exception as e:
+                        warning_logger(f"Failed to write SCIP call edge: {e}")
+
+    def delete_file_from_graph(self, path: str) -> None:
+        file_path_str = str(Path(path).resolve())
+        with self.driver.session() as session:
+            parents_res = session.run(
+                """
+                MATCH (f:File {path: $path})<-[:CONTAINS*]-(d:Directory)
+                RETURN d.path as path ORDER BY d.path DESC
+            """,
+                path=file_path_str,
+            )
+            parent_paths = [record["path"] for record in parents_res]
+
+            session.run(
+                """
+                MATCH (f:File {path: $path})
+                OPTIONAL MATCH (f)-[:CONTAINS]->(element)
+                DETACH DELETE f, element
+            """,
+                path=file_path_str,
+            )
+            info_logger(f"Deleted file and its elements from graph: {file_path_str}")
+
+            for p in parent_paths:
+                session.run(
+                    """
+                    MATCH (d:Directory {path: $path})
+                    WHERE NOT (d)-[:CONTAINS]->()
+                    DETACH DELETE d
+                """,
+                    path=p,
+                )
+
+    def delete_repository_from_graph(self, repo_path: str) -> bool:
+        repo_path_str = str(Path(repo_path).resolve())
+        path_prefix = repo_path_str + "/"
+        with self.driver.session() as session:
+            result = session.run(
+                "MATCH (r:Repository {path: $path}) RETURN count(r) as cnt", path=repo_path_str
+            ).single()
+            if not result or result["cnt"] == 0:
+                warning_logger(f"Attempted to delete non-existent repository: {repo_path_str}")
+                return False
+
+        for rel_type in ("CALLS", "INHERITS", "IMPORTS"):
+            while True:
+                with self.driver.session() as session:
+                    result = session.run(
+                        f"MATCH (a)-[r:{rel_type}]->(b) "
+                        "WHERE a.path STARTS WITH $prefix OR b.path STARTS WITH $prefix "
+                        "WITH r LIMIT 5000 DELETE r RETURN count(r) AS deleted",
+                        prefix=path_prefix,
+                    ).single()
+                    deleted = result["deleted"] if result else 0
+                if deleted == 0:
+                    break
+                info_logger(f"[DELETE] Removed {deleted} {rel_type} rels for {repo_path_str}")
+
+        while True:
+            with self.driver.session() as session:
+                result = session.run(
+                    "MATCH (a)-[r:CONTAINS]->(b) "
+                    "WHERE a.path STARTS WITH $prefix OR a.path = $path "
+                    "WITH r LIMIT 10000 DELETE r RETURN count(r) AS deleted",
+                    prefix=path_prefix,
+                    path=repo_path_str,
+                ).single()
+                deleted = result["deleted"] if result else 0
+            if deleted == 0:
+                break
+            info_logger(f"[DELETE] Removed {deleted} CONTAINS rels for {repo_path_str}")
+
+        for label in ("Function", "Class", "File"):
+            while True:
+                with self.driver.session() as session:
+                    result = session.run(
+                        f"MATCH (n:{label}) WHERE n.path STARTS WITH $prefix "
+                        "WITH n LIMIT 10000 DETACH DELETE n RETURN count(n) AS deleted",
+                        prefix=path_prefix,
+                    ).single()
+                    deleted = result["deleted"] if result else 0
+                if deleted == 0:
+                    break
+                info_logger(f"[DELETE] Removed {deleted} {label} nodes for {repo_path_str}")
+
+        with self.driver.session() as session:
+            session.run("MATCH (r:Repository {path: $path}) DETACH DELETE r", path=repo_path_str)
+
+        info_logger(f"Deleted repository and its contents from graph: {repo_path_str}")
+        return True
+
+    def get_caller_file_paths(self, file_path_str: str) -> set:
+        with self.driver.session() as session:
+            result = session.run(
+                "MATCH (caller)-[:CALLS]->(callee) "
+                "WHERE callee.path = $path "
+                "RETURN DISTINCT coalesce(caller.path, '') AS p",
+                path=file_path_str,
+            )
+            return {r["p"] for r in result if r["p"] and r["p"] != file_path_str}
+
+    def get_inheritance_neighbor_paths(self, file_path_str: str) -> set:
+        with self.driver.session() as session:
+            result = session.run(
+                "MATCH (a)-[:INHERITS]->(b) "
+                "WHERE a.path = $path OR b.path = $path "
+                "RETURN DISTINCT CASE WHEN a.path = $path THEN b.path ELSE a.path END AS p",
+                path=file_path_str,
+            )
+            return {r["p"] for r in result if r["p"] and r["p"] != file_path_str}
+
+    def delete_outgoing_calls_from_files(self, file_paths: List[str]) -> None:
+        with self.driver.session() as session:
+            result = session.run(
+                "MATCH (a)-[r:CALLS]->(b) WHERE a.path IN $paths DELETE r RETURN count(r) AS cnt",
+                paths=file_paths,
+            ).single()
+            cnt = result["cnt"] if result else 0
+        info_logger(f"[RELINK] Deleted {cnt} outgoing CALLS from {len(file_paths)} caller files")
+
+    def delete_inherits_for_files(self, file_paths: List[str]) -> None:
+        with self.driver.session() as session:
+            result = session.run(
+                "MATCH (a)-[r:INHERITS]->(b) WHERE a.path IN $paths OR b.path IN $paths "
+                "DELETE r RETURN count(r) AS cnt",
+                paths=file_paths,
+            ).single()
+            cnt = result["cnt"] if result else 0
+        info_logger(f"[RELINK] Deleted {cnt} INHERITS for {len(file_paths)} affected files")
+
+    def get_repo_class_lookup(self, repo_path: Path) -> Dict[str, set]:
+        prefix = str(repo_path.resolve()) + "/"
+        result_map: Dict[str, set] = {}
+        with self.driver.session() as session:
+            result = session.run(
+                "MATCH (c:Class) WHERE c.path STARTS WITH $prefix "
+                "RETURN c.name AS name, c.path AS path",
+                prefix=prefix,
+            )
+            for record in result:
+                path = record["path"]
+                if path not in result_map:
+                    result_map[path] = set()
+                result_map[path].add(record["name"])
+        return result_map
+
+    def delete_relationship_links(self, repo_path: Path) -> None:
+        repo_path_str = str(repo_path.resolve()) + "/"
+        with self.driver.session() as session:
+            result = session.run(
+                "MATCH (a)-[r:CALLS]->(b) WHERE a.path STARTS WITH $prefix DELETE r RETURN count(r) AS cnt",
+                prefix=repo_path_str,
+            ).single()
+            calls_deleted = result["cnt"] if result else 0
+
+            result = session.run(
+                "MATCH (a)-[r:INHERITS]->(b) WHERE a.path STARTS WITH $prefix DELETE r RETURN count(r) AS cnt",
+                prefix=repo_path_str,
+            ).single()
+            inherits_deleted = result["cnt"] if result else 0
+
+        info_logger(
+            f"[RELINK] Cleared {calls_deleted} CALLS and {inherits_deleted} INHERITS before re-linking: {repo_path}"
+        )