mirror of
https://github.com/agentscope-ai/ReMe.git
synced 2026-09-22 00:32:49 +00:00
b72690d954
- add neo4j dependency to project requirements - introduce NetworkXFileGraph to replace LocalFileGraph implementation - rename local_file_graph.py to networkx_file_graph.py with updated component registration as 'networkx' - remove pickle persistence logic from NetworkX backend, simplify initialization - update Neo4jFileGraph to return FileLink objects instead of (FileNode, FileLink) tuples from get_inlinks/get_outlinks methods - remove unused AsyncIterator import and adjust method signatures - add BareFileParser for handling binary/attachment files without content parsing - move wikilink resolution utilities to dedicated utility module - refactor memory I/O to use file graph's link resolution methods directly - remove link extraction utilities from schema module, consolidate in utils.wikilink_resolver
663 lines
22 KiB
Python
663 lines
22 KiB
Python
"""Memory File System engine API — the core engine's outward surface.
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The .md files are the SSOT (per `structure.md` §"核心引擎"). The engine
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is layered:
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Memory File System → Watcher & Parser → Projections (vector / FTS)
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(write entry) (incremental) (read entry, derived)
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This module is the **single public API surface** over that engine. Every
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consumer — agent-facing steps, the three memory services (Retriever,
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Ingestor, Maintainer), and the toolkit (`memory_toolkit`) — talks to
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the engine through these functions, not by reaching into
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``BaseFileStore`` directly.
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Layering note. The slim ``BaseFileStore`` interface only owns the
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search projections (vector / FTS) plus atomic file upserts/deletes.
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Iteration, single-node lookup, and the wikilink graph live HERE — we
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walk ``LocalFileStore._nodes`` directly (engine-layer peer) and compute
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links on-the-fly from each ``FileNode.links``. There is no precomputed
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graph index; the graph is a derivation of the SSoT.
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Naming convention:
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- Verb-first: `get_file`, `create_file`, `search_vector`.
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- `file_store` is always the first positional argument when the
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function needs the engine handle; remaining args are keyword-only.
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- Pure-disk writes (`update_body`, `update_meta`, `delete_file`,
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`archive_file`) don't take `file_store` — they hit the filesystem
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and the watcher picks them up. The asymmetry is honest.
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"""
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from __future__ import annotations
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import re
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import shutil
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from collections import deque
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from collections.abc import Iterable, Iterator
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from pathlib import Path
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import frontmatter
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from ..component.file_store.base_file_store import BaseFileStore
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from ..schema import ChunkFilter, FileChunk, FileNode
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from ..utils.wikilink_resolver import (
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_WIKILINK_RE,
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extract_wikilinks,
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)
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# ===========================================================================
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# Internal helpers — engine-layer access to the concrete node index
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# ===========================================================================
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#
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# ``BaseFileStore`` only declares the search/upsert contract; iteration
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# and single-node lookup live on the concrete impl (``LocalFileStore``).
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# memory_io is a peer at the engine layer, so reaching into ``_nodes``
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# is intentional — every iteration / graph walk funnels through here so
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# the day the engine grows a public ``iter_nodes()``, this is the only
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# place to swap.
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def _meta(node: FileNode) -> dict:
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"""Full frontmatter dict for a node — typed fields (title/description/
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tags) merged with any ``extra=allow`` extras."""
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return node.front_matter.model_dump()
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def _filter_to_dict(chunk_filter: ChunkFilter | None) -> dict:
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"""Serialize ``ChunkFilter`` for the search engine's ``search_filter`` arg."""
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if chunk_filter is None:
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return {}
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return chunk_filter.model_dump(mode="json")
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# ===========================================================================
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# Section 1 — MFS Reads
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# ===========================================================================
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async def get_file(
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file_store: BaseFileStore,
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path: str,
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*,
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include_chunks: bool = False,
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) -> dict:
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"""Read frontmatter + body for one path. Optionally include parsed chunks.
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On-disk frontmatter is the source of truth — the file_store cache may
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lag a write that hasn't been picked up by the watcher yet.
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"""
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node = await file_store.get_node_by_path(path) # type: ignore[attr-defined]
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result: dict = {"path": path, "exists": False}
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if node is not None:
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result.update(
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{
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"exists": True,
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"metadata": _meta(node),
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"link": [link.model_dump(exclude_none=True) for link in node.links],
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}
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)
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file_path = Path(path)
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if file_path.is_file():
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raw = file_path.read_text(encoding="utf-8")
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post = frontmatter.loads(raw)
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result["exists"] = True
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result["content"] = post.content
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result["metadata"] = dict(post.metadata)
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if include_chunks:
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chunks = await file_store.get_chunks_by_path(path) # type: ignore[attr-defined]
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result["chunks"] = [c.model_dump(exclude_none=True) for c in chunks]
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return result
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def list_files(
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file_store: BaseFileStore,
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*,
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path_prefix: str | None = None,
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tags: list[str] | None = None,
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metadata: dict | None = None,
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limit: int = 100,
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) -> dict:
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"""List indexed files filtered by frontmatter exact-match, tags, and prefix."""
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metadata_filter = metadata or {}
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tag_filter = tags or []
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items: list[dict] = []
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for path, node in _nodes(file_store).items():
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if path_prefix and not path.startswith(path_prefix):
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continue
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md = _meta(node)
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if metadata_filter and any(md.get(k) != v for k, v in metadata_filter.items()):
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continue
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if tag_filter:
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file_tags = set(md.get("tags") or [])
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if not all(t in file_tags for t in tag_filter):
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continue
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items.append({"path": path, "metadata": md})
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if len(items) >= limit:
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break
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return {"items": items, "count": len(items)}
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def get_inlinks(file_store: BaseFileStore, path: str) -> dict:
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"""Files that `path` links TO (resolved). Each entry carries the typed-link predicate."""
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return {
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"path": path,
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"inlinks": file_store.file_graph.get_inlinks(path),
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}
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def get_outlinks(file_store: BaseFileStore, path: str) -> dict:
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"""Files that link TO `path`. Each entry carries the typed-link predicate."""
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return {
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"path": path,
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"outlinks": file_store.file_graph.get_outlinks(path),
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}
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def resolve_wikilink(file_store: BaseFileStore, wikilink: str) -> dict:
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"""Resolve a `[[target]]` wikilink with full ambiguity context.
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Returns:
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unique resolution → {wikilink, path, exists: True,
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ambiguous: False, candidates: [path]}
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ambiguous → {wikilink, path: None, exists: False,
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ambiguous: True, candidates: [...]}
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dangling → {wikilink, path: None, exists: False,
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ambiguous: False, candidates: []}
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"""
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if "/" in wikilink or wikilink.endswith(".md"):
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hit = _resolve_wikilink(file_store, wikilink)
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return {
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"wikilink": wikilink,
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"path": hit,
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"exists": hit is not None,
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"ambiguous": False,
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"candidates": [hit] if hit else [],
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}
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candidates = wikilink_candidates(file_store, wikilink)
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if len(candidates) == 1:
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return {
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"wikilink": wikilink,
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"path": candidates[0],
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"exists": True,
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"ambiguous": False,
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"candidates": candidates,
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}
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return {
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"wikilink": wikilink,
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"path": None,
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"exists": False,
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"ambiguous": len(candidates) > 1,
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"candidates": candidates,
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}
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def iter_files(file_store: BaseFileStore) -> Iterator[tuple[str, FileNode]]:
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"""Walk every indexed (path, FileNode). Used by Maintainer scans."""
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return iter(_nodes(file_store).items())
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async def count_tokens(
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token_counter,
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*,
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path: str | None = None,
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text: str | None = None,
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) -> dict:
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"""Estimate tokens for a file body (frontmatter excluded) or raw text."""
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if path:
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target = Path(path)
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if not target.is_file():
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return {"path": str(target), "error": "file not found"}
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raw = target.read_text(encoding="utf-8")
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post = frontmatter.loads(raw)
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body = post.content
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tokens = await token_counter.count(messages=[], text=body)
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return {
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"source": "file",
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"path": str(target.resolve()),
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"tokens": tokens,
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"body_chars": len(body),
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}
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if text:
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tokens = await token_counter.count(messages=[], text=text)
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return {
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"source": "text",
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"tokens": tokens,
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"body_chars": len(text),
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}
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return {"error": "one of `path` or `text` is required"}
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# ===========================================================================
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# Section 2 — MFS Writes
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# ===========================================================================
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def _replace_wikilink_targets(text: str, mapping: dict[str, str]) -> str:
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"""Rewrite wikilink targets in raw text. Anchors / aliases / embed prefix kept."""
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if not mapping:
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return text
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def sub(m: re.Match) -> str:
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target_raw = m.group(1)
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target = target_raw.strip()
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if target in mapping:
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return m.group(0).replace(target_raw, mapping[target], 1)
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return m.group(0)
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return _WIKILINK_RE.sub(sub, text)
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def create_file(
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file_store: BaseFileStore,
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path: Path,
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*,
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metadata: dict,
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content: str,
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overwrite: bool = False,
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force: bool = False,
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) -> tuple[bool, dict]:
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"""Single L1 entry point for creating a markdown file.
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Refuses when:
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- file already exists (unless overwrite=True)
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- creating it would make `[[stem]]` ambiguous (unless force=True)
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"""
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if path.exists() and not overwrite:
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return False, {"path": str(path), "error": "file already exists"}
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if not force:
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conflicts = collisions_after_create(file_store, path)
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if conflicts:
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return False, {
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"path": str(path),
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"error": (
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f"stem `[[{path.stem}]]` would resolve ambiguously "
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f"to {len(conflicts) + 1} paths after this create"
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),
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"conflicts": conflicts,
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"hint": (
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f"either rename to a unique stem, or have callers "
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f"link via the explicit-path form "
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f"`[[{path.parent.name}/{path.stem}]]`; pass "
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f"force=true only if you accept the ambiguity"
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),
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}
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path.parent.mkdir(parents=True, exist_ok=True)
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post = frontmatter.Post(content, **metadata)
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path.write_text(frontmatter.dumps(post), encoding="utf-8")
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return True, {"path": str(path), "created": True}
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def update_body(
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path: Path | str,
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*,
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old_string: str,
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new_string: str,
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replace_all: bool = False,
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) -> tuple[bool, dict]:
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"""Edit-style content update — replace `old_string` with `new_string`."""
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target = Path(path)
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if not target.is_file():
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return False, {"path": str(target), "error": "file not found"}
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if not old_string:
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return False, {
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"path": str(target),
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"error": "old_string is required (use create_file to write a new file)",
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}
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raw = target.read_text(encoding="utf-8")
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occurrences = raw.count(old_string)
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if occurrences == 0:
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return False, {"path": str(target), "error": "old_string not found in file"}
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if occurrences > 1 and not replace_all:
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return False, {
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"path": str(target),
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"error": f"old_string appears {occurrences} times; pass replace_all=true to replace all",
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"occurrences": occurrences,
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}
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if replace_all:
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new_raw = raw.replace(old_string, new_string)
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else:
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new_raw = raw.replace(old_string, new_string, 1)
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target.write_text(new_raw, encoding="utf-8")
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return True, {
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"path": str(target),
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"replaced": occurrences if replace_all else 1,
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}
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def update_meta(path: Path | str, *, key: str, value) -> tuple[bool, dict]:
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"""Update a single YAML frontmatter key. value=None deletes the key."""
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target = Path(path)
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if not target.is_file():
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return False, {"path": str(target), "error": "file not found"}
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raw = target.read_text(encoding="utf-8")
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post = frontmatter.loads(raw)
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if value is None:
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post.metadata.pop(key, None)
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else:
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post.metadata[key] = value
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target.write_text(frontmatter.dumps(post), encoding="utf-8")
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return True, {"path": str(target), "key": key, "value": value}
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def rename_file(
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file_store: BaseFileStore,
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working_dir: Path | str,
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*,
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old_path: Path | str,
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new_path: Path | str,
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) -> tuple[bool, dict]:
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"""Rename a file and rewrite incoming wikilinks across the vault."""
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old_p = Path(old_path).resolve()
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new_p = Path(new_path).resolve()
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if not old_p.is_file():
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return False, {"old_path": str(old_p), "error": "old_path not found"}
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if new_p.exists():
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return False, {"new_path": str(new_p), "error": "new_path already exists"}
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if old_p == new_p:
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return False, {"error": "old_path and new_path are the same"}
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conflicts = collisions_after_create(file_store, new_p)
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if conflicts:
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return False, {
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"error": (
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f"stem `[[{new_p.stem}]]` would resolve ambiguously " f"to {len(conflicts) + 1} paths after this rename"
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),
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"conflicts": conflicts,
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"hint": (
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f"either rename to a unique stem (consider a "
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f"domain-specific suffix), or have callers link via "
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f"the explicit-path form `[[{new_p.parent.name}/{new_p.stem}]]`"
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),
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}
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working_dir_p = Path(working_dir).resolve()
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old_stem = old_p.stem
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new_stem = new_p.stem
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replacements: dict[str, str] = {}
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if old_stem != new_stem:
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replacements[old_stem] = new_stem
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try:
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old_rel = str(old_p.relative_to(working_dir_p).with_suffix(""))
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new_rel = str(new_p.relative_to(working_dir_p).with_suffix(""))
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if old_rel != new_rel:
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replacements[old_rel] = new_rel
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replacements[old_rel + ".md"] = new_rel + ".md"
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except ValueError:
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pass
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referring_paths = [m.path for m, _ in _get_inlinks(file_store, str(old_p))]
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new_p.parent.mkdir(parents=True, exist_ok=True)
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old_p.rename(new_p)
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updated_files: list[str] = []
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write_errors: list[dict] = []
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if replacements and referring_paths:
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for path in referring_paths:
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file_path = Path(path)
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if not file_path.is_file():
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continue
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try:
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raw = file_path.read_text(encoding="utf-8")
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new_raw = _replace_wikilink_targets(raw, replacements)
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if new_raw != raw:
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file_path.write_text(new_raw, encoding="utf-8")
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updated_files.append(path)
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except Exception as exc:
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write_errors.append({"path": path, "error": str(exc)})
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return True, {
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"old_path": str(old_p),
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"new_path": str(new_p),
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"stem_changed": old_stem != new_stem,
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"replacements": replacements,
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"referring_count": len(referring_paths),
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"updated_files": updated_files,
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"write_errors": write_errors,
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}
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def delete_file(path: Path | str) -> tuple[bool, dict]:
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"""Delete a file. Watcher removes from store + graph."""
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target = Path(path)
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if not target.exists():
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return False, {"path": str(target), "error": "not found"}
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target.unlink()
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return True, {"path": str(target), "deleted": True}
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def archive_file(
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working_dir: Path | str,
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path: Path | str,
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*,
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archive_dir: str = "Archive",
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) -> tuple[bool, dict]:
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"""Archive a file: flip `status: archived`, then move under `<vault>/<archive_dir>/`."""
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src = Path(path).resolve()
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if not src.is_file():
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return False, {"path": str(src), "error": "file not found"}
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vault = Path(working_dir).resolve()
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try:
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rel = src.relative_to(vault)
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except ValueError:
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return False, {
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"path": str(src),
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"error": f"path is outside working_dir {vault}",
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}
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dst = vault / archive_dir / rel
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if dst.exists():
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return False, {
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"path": str(src),
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"error": f"archive destination already exists: {dst}",
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}
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ok, prop_payload = update_meta(src, key="status", value="archived")
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if not ok:
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return False, {**prop_payload, "stage": "update_meta"}
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dst.parent.mkdir(parents=True, exist_ok=True)
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try:
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shutil.move(str(src), str(dst))
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except OSError as exc:
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return False, {
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"path": str(src),
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"error": f"move failed: {exc}",
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"stage": "move",
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}
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return True, {
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"old_path": str(src),
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"new_path": str(dst),
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"archived": True,
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}
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# ===========================================================================
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# Section 3 — Projection Queries
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# ===========================================================================
|
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|
|
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async def search_vector(
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file_store: BaseFileStore,
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query: str,
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*,
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limit: int,
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chunk_filter: ChunkFilter | None = None,
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) -> list[FileChunk]:
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"""Vector similarity over the chunk-level Vector projection."""
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return await file_store.vector_search(query, limit, _filter_to_dict(chunk_filter))
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|
|
|
|
|
async def search_keyword(
|
|
file_store: BaseFileStore,
|
|
query: str,
|
|
*,
|
|
limit: int,
|
|
chunk_filter: ChunkFilter | None = None,
|
|
) -> list[FileChunk]:
|
|
"""FTS5 keyword search over the chunk-level keyword projection."""
|
|
return await file_store.keyword_search(query, limit, _filter_to_dict(chunk_filter))
|
|
|
|
|
|
async def get_chunks(
|
|
file_store: BaseFileStore,
|
|
paths: Iterable[str],
|
|
) -> list[FileChunk]:
|
|
"""Batch fetch chunks across many paths."""
|
|
out: list[FileChunk] = []
|
|
for p in paths:
|
|
out.extend(await file_store.get_chunks_by_path(p)) # type: ignore[attr-defined]
|
|
return out
|
|
|
|
|
|
# ===========================================================================
|
|
# Section 4 — Graph helpers (BFS / scoring / collisions)
|
|
# ===========================================================================
|
|
#
|
|
# All graph traversal walks ``FileNode.links`` directly via ``_get_outlinks``
|
|
# / ``_get_inlinks``. There's no precomputed adjacency index — every BFS
|
|
# resolves wikilinks per call. Cheap enough for typical vault sizes;
|
|
# revisit if the maintainer's lint pass becomes a hotspot.
|
|
|
|
|
|
def expand_neighbors(
|
|
file_store: BaseFileStore,
|
|
seeds: Iterable[str],
|
|
*,
|
|
depth: int = 1,
|
|
direction: str = "both",
|
|
per_node_cap: int | None = 50,
|
|
) -> dict[str, int]:
|
|
"""BFS over wikilink edges. Returns `{path: hop_distance}`."""
|
|
if direction not in ("out", "in", "both"):
|
|
raise ValueError(f"direction must be one of out/in/both, got {direction!r}")
|
|
if depth < 0:
|
|
raise ValueError(f"depth must be >= 0, got {depth}")
|
|
|
|
nodes = _nodes(file_store)
|
|
seen: dict[str, int] = {}
|
|
frontier: deque[tuple[str, int]] = deque()
|
|
for path in seeds:
|
|
if path in nodes and path not in seen:
|
|
seen[path] = 0
|
|
frontier.append((path, 0))
|
|
|
|
while frontier:
|
|
path, dist = frontier.popleft()
|
|
if dist >= depth:
|
|
continue
|
|
|
|
neighbors: list[str] = []
|
|
if direction in ("out", "both"):
|
|
neighbors.extend(m.path for m, _ in _get_outlinks(file_store, path))
|
|
if direction in ("in", "both"):
|
|
neighbors.extend(m.path for m, _ in _get_inlinks(file_store, path))
|
|
|
|
if per_node_cap is not None and len(neighbors) > per_node_cap:
|
|
neighbors = neighbors[:per_node_cap]
|
|
|
|
for nb in neighbors:
|
|
if nb in seen:
|
|
continue
|
|
seen[nb] = dist + 1
|
|
frontier.append((nb, dist + 1))
|
|
|
|
return seen
|
|
|
|
|
|
def subgraph_score(
|
|
file_store: BaseFileStore,
|
|
seeds: Iterable[str],
|
|
*,
|
|
decay: float = 0.5,
|
|
depth: int = 1,
|
|
direction: str = "both",
|
|
per_node_cap: int | None = 50,
|
|
) -> dict[str, float]:
|
|
"""Decayed score per path: seed=1.0, 1-hop=decay, 2-hop=decay²..."""
|
|
if not (0.0 <= decay <= 1.0):
|
|
raise ValueError(f"decay must be in [0, 1], got {decay}")
|
|
hops = expand_neighbors(
|
|
file_store,
|
|
seeds,
|
|
depth=depth,
|
|
direction=direction,
|
|
per_node_cap=per_node_cap,
|
|
)
|
|
return {path: decay**hop for path, hop in hops.items()}
|
|
|
|
|
|
def extract_anchors(file_store: BaseFileStore, text: str) -> list[str]:
|
|
"""Pull `[[X]]` anchors from `text` and resolve each (deduped)."""
|
|
seen: set[str] = set()
|
|
out: list[str] = []
|
|
for raw in extract_wikilinks(text):
|
|
hit = _resolve_wikilink(file_store, raw)
|
|
if hit is not None and hit not in seen:
|
|
seen.add(hit)
|
|
out.append(hit)
|
|
return out
|
|
|
|
|
|
def collisions_after_create(
|
|
file_store: BaseFileStore,
|
|
proposed_path: str | Path,
|
|
) -> list[str]:
|
|
"""Existing paths that would conflict with adding `proposed_path`.
|
|
|
|
Folder-note rule: if `proposed_path`'s parent dir name == its stem,
|
|
only colliding folder-notes are returned (siblings with the same
|
|
stem don't ambiguate). Otherwise both folder-notes AND stem hits
|
|
are returned.
|
|
"""
|
|
p = Path(proposed_path)
|
|
stem = p.stem
|
|
proposed_abs = str(p.resolve())
|
|
is_folder_note = p.parent.name == stem
|
|
|
|
folder_hits: list[str] = []
|
|
stem_hits: list[str] = []
|
|
for path in _nodes(file_store):
|
|
if path == proposed_abs:
|
|
continue
|
|
path_obj = Path(path)
|
|
if path_obj.stem != stem:
|
|
continue
|
|
if path_obj.parent.name == stem:
|
|
folder_hits.append(path)
|
|
else:
|
|
stem_hits.append(path)
|
|
|
|
if is_folder_note:
|
|
return folder_hits
|
|
return folder_hits + stem_hits
|
|
|
|
|
|
def make_filter(
|
|
file_store: BaseFileStore,
|
|
*,
|
|
paths: list[str] | None = None,
|
|
tags: list[str] | None = None,
|
|
exclude_paths: list[str] | None = None,
|
|
) -> ChunkFilter | None:
|
|
"""Compile a ChunkFilter against the file_store's path/tag indexes."""
|
|
cf = ChunkFilter(paths=paths, tags=tags, exclude_paths=exclude_paths)
|
|
if cf.is_empty():
|
|
return cf
|
|
cf.resolved_paths = {p for p, n in _nodes(file_store).items() if cf.match_metadata(p, _meta(n))}
|
|
return cf
|
|
|
|
|
|
def find_collisions(file_store: BaseFileStore) -> dict[str, list[str]]:
|
|
"""Every stem that resolves to >1 path. Used by Maintainer.lint."""
|
|
by_stem: dict[str, list[str]] = {}
|
|
for path in _nodes(file_store):
|
|
by_stem.setdefault(Path(path).stem, []).append(path)
|
|
return {s: ps for s, ps in by_stem.items() if len(ps) > 1}
|