feat(01-04): rewrite services/storage.py as async SQLAlchemy + MinIO orchestrator

- Replaced entire flat-file + filelock implementation with async ORM + MinIO
- All 14 DB-touching functions are async def accepting AsyncSession as first param
- load_settings/save_settings/mask_api_key/settings_masked remain sync (flat-file, Phase 2 will migrate)
- save_upload uses null-user D-03 sentinel; object_key via MinIO put_object
- update_document_topics auto-creates missing topics via create_topic deduplication
- No filelock, no METADATA_DIR/UPLOADS_DIR/TOPICS_FILE references remain
- Added __all__ listing all 18 public functions
- Updated conftest.py: removed filelock patching no longer needed
- Fixed test_object_key_schema: removed unused db_session param (SQLite INET type conflict)

backend/services/storage.py

@@ -1,173 +1,436 @@
+"""
+Async document/topic/settings storage service for DocuVault.
+
+This module replaces the legacy flat-file + filelock implementation with:
+  - Async SQLAlchemy ORM for document and topic persistence (PostgreSQL)
+  - MinIO SDK (via asyncio.to_thread) for binary object storage
+
+Public function names are PRESERVED from the old flat-file implementation so
+that api/documents.py and api/topics.py can be updated in Plan 05 with minimal
+changes (async def + await + session parameter).
+
+Settings functions (load_settings / save_settings) remain sync and flat-file
+backed in Phase 1 because the users.ai_provider / users.ai_model schema columns
+cannot be populated until Phase 2.
+# Phase 2 will migrate this to DB-backed per-user settings (D-03 deferred to
+# user-scoped column population).
+
+D-05: Storage service layer switched to PostgreSQL + MinIO.
+D-06: Object key schema: {user_id}/{document_id}/{uuid4()}{ext} — human filename in DB only.
+D-03: documents.user_id is None (nullable) in Phase 1 — no auth system yet.
+"""
+from __future__ import annotations
+
+import copy
 import json
+import sys
 import uuid
-import shutil
 from datetime import datetime, timezone
 from pathlib import Path
-from filelock import FileLock
+from typing import Optional
-from config import UPLOADS_DIR, METADATA_DIR, TOPICS_FILE, SETTINGS_FILE, DEFAULT_SETTINGS
+
+from sqlalchemy import select, delete
+from sqlalchemy import func as sql_func
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from config import DEFAULT_SETTINGS, SETTINGS_FILE
+from db.models import Document, DocumentTopic, Topic
+from storage import get_storage_backend
 
 
-# ── File locks ────────────────────────────────────────────────────────────────
+# ── Lazy singleton storage backend ────────────────────────────────────────────
 
-_topics_lock = FileLock(str(TOPICS_FILE) + ".lock")
+_storage = None
-_settings_lock = FileLock(str(SETTINGS_FILE) + ".lock")
+
+
+def _backend():
+    """Return the lazily-instantiated StorageBackend singleton.
+
+    Mirrors the module-level singleton behaviour of the old filelock objects so
+    the MinIO client is created once per process, not once per request.
+    """
+    global _storage
+    _storage = _storage or get_storage_backend()
+    return _storage
+
+
+# ── Private helpers ────────────────────────────────────────────────────────────
+
+def _doc_to_dict(doc: Document, topic_names: list) -> dict:
+    """Convert a Document ORM row + resolved topic names to the legacy dict shape."""
+    return {
+        "id": str(doc.id),
+        "original_name": doc.filename,
+        "filename": doc.filename,
+        "mime_type": doc.content_type,
+        "size_bytes": doc.size_bytes,
+        "extracted_text": doc.extracted_text or "",
+        "topics": topic_names,
+        "created_at": doc.created_at.isoformat() if doc.created_at else None,
+        "classified_at": doc.updated_at.isoformat() if doc.status == "classified" else None,
+    }
+
+
+async def _load_topic_names(session: AsyncSession, doc_id: uuid.UUID) -> list:
+    """Return the list of topic names for a given document UUID."""
+    q = await session.execute(
+        select(Topic.name)
+        .join(DocumentTopic, DocumentTopic.topic_id == Topic.id)
+        .where(DocumentTopic.document_id == doc_id)
+    )
+    return [row[0] for row in q]
 
 
 # ── Documents ─────────────────────────────────────────────────────────────────
 
-def save_upload(file_bytes: bytes, original_name: str, mime_type: str) -> dict:
+async def save_upload(
-    doc_id = str(uuid.uuid4())
+    session: AsyncSession,
+    file_bytes: bytes,
+    original_name: str,
+    mime_type: str,
+) -> dict:
+    """Persist file bytes to MinIO and create a Document row in PostgreSQL.
+
+    Returns a dict shape compatible with the legacy api/documents.py line 32–33:
+      {"id", "filename", "path", "object_key", "user_id"}
+
+    The "path" key is preserved for compatibility — it now contains the MinIO
+    object_key rather than a filesystem path.
+
+    D-03: user_id is None (no auth in Phase 1). Phase 2 will replace the
+    "null-user" sentinel with str(current_user.id).
+    """
+    doc_id = uuid.uuid4()
     suffix = Path(original_name).suffix.lower()
-    filename = f"{doc_id}{suffix}"
+
-    dest = UPLOADS_DIR / filename
+    doc = Document(
-    dest.write_bytes(file_bytes)
+        id=doc_id,
-    return {"id": doc_id, "filename": filename, "path": str(dest)}
+        user_id=None,  # D-03: nullable in Phase 1
+        filename=original_name,
+        content_type=mime_type,
+        size_bytes=len(file_bytes),
+        storage_backend="minio",
+        status="pending",
+        object_key="",  # filled after MinIO upload below
+    )
+    session.add(doc)
+    await session.flush()  # materialise doc.id without committing
+
+    # D-03: "null-user" sentinel — Phase 2 replaces with str(current_user.id)
+    object_key = await _backend().put_object(
+        user_id="null-user",
+        document_id=str(doc_id),
+        file_bytes=file_bytes,
+        extension=suffix,
+        content_type=mime_type,
+    )
+    doc.object_key = object_key
+    await session.commit()
+
+    return {
+        "id": str(doc_id),
+        "filename": original_name,
+        "path": object_key,
+        "object_key": object_key,
+        "user_id": None,
+    }
 
 
-def save_metadata(meta: dict) -> None:
+async def save_metadata(session: AsyncSession, meta: dict) -> None:
-    path = METADATA_DIR / f"{meta['id']}.json"
+    """Update a Document row from the legacy metadata dict shape.
-    lock = FileLock(str(path) + ".lock")
-    with lock:
-        path.write_text(json.dumps(meta, indent=2, ensure_ascii=False))
 
-
+    Keys consumed: id, extracted_text, topics (list[str]), classified_at.
-def get_metadata(doc_id: str) -> dict | None:
+    """
-    path = METADATA_DIR / f"{doc_id}.json"
-    if not path.exists():
-        return None
-    return json.loads(path.read_text())
-
-
-def list_metadata(topic: str | None = None) -> list[dict]:
-    docs = []
-    for p in sorted(METADATA_DIR.glob("*.json"), key=lambda x: x.stat().st_mtime, reverse=True):
     try:
-            meta = json.loads(p.read_text())
+        uid = uuid.UUID(meta["id"])
-        except Exception:
+    except (ValueError, KeyError):
-            continue
+        return
-        if topic and topic not in meta.get("topics", []):
+
-            continue
+    doc = await session.get(Document, uid)
-        docs.append(meta)
+    if doc is None:
-    return docs
+        return
+
+    doc.extracted_text = meta.get("extracted_text", "")
+
+    topics_list = meta.get("topics")
+    if topics_list:
+        await update_document_topics(session, meta["id"], topics_list)
+
+    doc.status = "classified" if meta.get("classified_at") else "pending"
+    await session.commit()
 
 
-def delete_document(doc_id: str) -> bool:
+async def get_metadata(session: AsyncSession, doc_id: str) -> Optional[dict]:
-    meta_path = METADATA_DIR / f"{doc_id}.json"
+    """Return the legacy metadata dict for a document, or None if not found."""
-    if not meta_path.exists():
+    try:
+        uid = uuid.UUID(doc_id)
+    except ValueError:
+        return None
+
+    doc = await session.get(Document, uid)
+    if doc is None:
+        return None
+
+    topic_names = await _load_topic_names(session, uid)
+    return _doc_to_dict(doc, topic_names)
+
+
+async def list_metadata(
+    session: AsyncSession, topic: Optional[str] = None
+) -> list:
+    """Return a list of metadata dicts, optionally filtered by topic name."""
+    stmt = select(Document).order_by(Document.created_at.desc())
+    if topic is not None:
+        stmt = (
+            stmt.join(DocumentTopic, DocumentTopic.document_id == Document.id)
+            .join(Topic, Topic.id == DocumentTopic.topic_id)
+            .where(Topic.name == topic)
+        )
+    result = await session.execute(stmt)
+    docs = result.scalars().all()
+
+    rows = []
+    for doc in docs:
+        topic_names = await _load_topic_names(session, doc.id)
+        rows.append(_doc_to_dict(doc, topic_names))
+    return rows
+
+
+async def delete_document(session: AsyncSession, doc_id: str) -> bool:
+    """Delete a document's MinIO object and its PostgreSQL row.
+
+    Returns False if the document is not found; True on success.
+    MinIO deletion failures are logged to stderr but do not prevent the DB row
+    deletion (the bytes may already be gone).
+    """
+    try:
+        uid = uuid.UUID(doc_id)
+    except ValueError:
         return False
-    meta = json.loads(meta_path.read_text())
+
-    upload_path = UPLOADS_DIR / meta.get("filename", "")
+    doc = await session.get(Document, uid)
-    if upload_path.exists():
+    if doc is None:
-        upload_path.unlink()
+        return False
-    meta_path.unlink()
+
-    lock_path = Path(str(meta_path) + ".lock")
+    try:
-    if lock_path.exists():
+        await _backend().delete_object(doc.object_key)
-        lock_path.unlink()
+    except Exception as exc:
+        print(f"[storage] WARNING: MinIO delete_object failed for {doc.object_key!r}: {exc}", file=sys.stderr)
+
+    await session.delete(doc)
+    await session.commit()
     return True
 
 
-def update_document_topics(doc_id: str, topics: list[str]) -> dict | None:
+async def update_document_topics(
-    meta = get_metadata(doc_id)
+    session: AsyncSession, doc_id: str, topics: list
-    if meta is None:
+) -> Optional[dict]:
-        return None
+    """Replace all topic associations for a document.
-    meta["topics"] = topics
-    meta["classified_at"] = datetime.now(timezone.utc).isoformat()
-    save_metadata(meta)
-    return meta
 
-
+    Auto-creates topics that don't yet exist. Returns the refreshed metadata
-def remove_topic_from_all_documents(topic_name: str) -> int:
+    dict, or None if the document is not found.
-    """Remove a topic name from all documents. Returns number of docs updated."""
+    """
-    count = 0
-    for p in METADATA_DIR.glob("*.json"):
     try:
-            meta = json.loads(p.read_text())
+        uid = uuid.UUID(doc_id)
-        except Exception:
+    except ValueError:
+        return None
+
+    doc = await session.get(Document, uid)
+    if doc is None:
+        return None
+
+    # Remove all existing associations
+    await session.execute(
+        delete(DocumentTopic).where(DocumentTopic.document_id == uid)
+    )
+
+    # Re-insert, deduplicating by name
+    seen: set = set()
+    for name in topics:
+        if name in seen:
             continue
-        if topic_name in meta.get("topics", []):
+        seen.add(name)
-            meta["topics"] = [t for t in meta["topics"] if t != topic_name]
+        topic_dict = await create_topic(session, name)
-            lock = FileLock(str(p) + ".lock")
+        session.add(
-            with lock:
+            DocumentTopic(
-                p.write_text(json.dumps(meta, indent=2, ensure_ascii=False))
+                document_id=uid,
-            count += 1
+                topic_id=uuid.UUID(topic_dict["id"]),
-    return count
+            )
+        )
+
+    doc.status = "classified"
+    await session.commit()
+    return await get_metadata(session, doc_id)
+
+
+async def remove_topic_from_all_documents(
+    session: AsyncSession, topic_name: str
+) -> int:
+    """Delete all DocumentTopic rows for the named topic.
+
+    Returns the number of rows deleted.
+    """
+    q = await session.execute(
+        select(Topic).where(sql_func.lower(Topic.name) == topic_name.lower())
+    )
+    topic = q.scalars().first()
+    if topic is None:
+        return 0
+
+    result = await session.execute(
+        delete(DocumentTopic).where(DocumentTopic.topic_id == topic.id)
+    )
+    await session.commit()
+    return result.rowcount
 
 
 # ── Topics ────────────────────────────────────────────────────────────────────
 
-def load_topics() -> list[dict]:
+async def load_topics(session: AsyncSession) -> list:
-    with _topics_lock:
+    """Return all topics ordered by name."""
-        data = json.loads(TOPICS_FILE.read_text())
+    q = await session.execute(select(Topic).order_by(Topic.name))
-    return data.get("topics", [])
+    return [
+        {"id": str(t.id), "name": t.name, "description": t.description, "color": t.color}
+        for t in q.scalars()
+    ]
 
 
-def save_topics(topics: list[dict]) -> None:
+async def save_topics(session: AsyncSession, topics: list) -> None:
-    with _topics_lock:
+    """Idempotent bulk replace — delete all Topic rows then insert the list.
-        TOPICS_FILE.write_text(json.dumps({"topics": topics}, indent=2))
 
-
+    # legacy: not used by current endpoints; preserved for API compatibility.
-def get_topic(topic_id: str) -> dict | None:
+    """
-    return next((t for t in load_topics() if t["id"] == topic_id), None)
+    await session.execute(delete(Topic))
-
-
-def create_topic(name: str, description: str = "", color: str = "#6366f1") -> dict:
-    topics = load_topics()
-    # Deduplicate by name (case-insensitive)
-    if any(t["name"].lower() == name.lower() for t in topics):
-        return next(t for t in topics if t["name"].lower() == name.lower())
-    topic = {
-        "id": str(uuid.uuid4())[:8],
-        "name": name,
-        "description": description,
-        "color": color,
-    }
-    topics.append(topic)
-    save_topics(topics)
-    return topic
-
-
-def update_topic(topic_id: str, **kwargs) -> dict | None:
-    topics = load_topics()
     for t in topics:
-        if t["id"] == topic_id:
+        session.add(
-            t.update({k: v for k, v in kwargs.items() if v is not None})
+            Topic(
-            save_topics(topics)
+                id=uuid.UUID(t["id"]) if t.get("id") else uuid.uuid4(),
-            return t
+                name=t["name"],
-    return None
+                description=t.get("description", ""),
+                color=t.get("color", "#6366f1"),
+            )
+        )
+    await session.commit()
 
 
-def delete_topic(topic_id: str) -> str | None:
+async def get_topic(session: AsyncSession, topic_id: str) -> Optional[dict]:
-    topics = load_topics()
+    """Return a topic dict by UUID string, or None if not found."""
-    topic = next((t for t in topics if t["id"] == topic_id), None)
+    try:
-    if not topic:
+        uid = uuid.UUID(topic_id)
+    except ValueError:
         return None
-    name = topic["name"]
+    t = await session.get(Topic, uid)
-    save_topics([t for t in topics if t["id"] != topic_id])
+    if t is None:
-    remove_topic_from_all_documents(name)
+        return None
+    return {"id": str(t.id), "name": t.name, "description": t.description, "color": t.color}
+
+
+async def create_topic(
+    session: AsyncSession,
+    name: str,
+    description: str = "",
+    color: str = "#6366f1",
+) -> dict:
+    """Create a topic, or return the existing one (case-insensitive deduplication)."""
+    q = await session.execute(
+        select(Topic).where(sql_func.lower(Topic.name) == name.lower())
+    )
+    existing = q.scalars().first()
+    if existing is not None:
+        return {
+            "id": str(existing.id),
+            "name": existing.name,
+            "description": existing.description,
+            "color": existing.color,
+        }
+
+    topic = Topic(name=name, description=description, color=color)
+    session.add(topic)
+    await session.commit()
+    return {
+        "id": str(topic.id),
+        "name": topic.name,
+        "description": topic.description,
+        "color": topic.color,
+    }
+
+
+async def update_topic(
+    session: AsyncSession,
+    topic_id: str,
+    name: Optional[str] = None,
+    description: Optional[str] = None,
+    color: Optional[str] = None,
+) -> Optional[dict]:
+    """Update non-None fields on a topic. Returns updated dict or None."""
+    try:
+        uid = uuid.UUID(topic_id)
+    except ValueError:
+        return None
+    t = await session.get(Topic, uid)
+    if t is None:
+        return None
+    if name is not None:
+        t.name = name
+    if description is not None:
+        t.description = description
+    if color is not None:
+        t.color = color
+    await session.commit()
+    return {"id": str(t.id), "name": t.name, "description": t.description, "color": t.color}
+
+
+async def delete_topic(session: AsyncSession, topic_id: str) -> Optional[str]:
+    """Delete a topic and cascade-remove its DocumentTopic rows.
+
+    Returns the deleted topic name, or None if not found.
+    """
+    try:
+        uid = uuid.UUID(topic_id)
+    except ValueError:
+        return None
+    t = await session.get(Topic, uid)
+    if t is None:
+        return None
+    name = t.name
+    await session.delete(t)  # ondelete="CASCADE" removes DocumentTopic rows
+    await session.commit()
     return name
 
 
-def topic_doc_counts() -> dict[str, int]:
+async def topic_doc_counts(session: AsyncSession) -> dict:
-    counts: dict[str, int] = {}
+    """Return a mapping of topic name -> document count."""
-    for p in METADATA_DIR.glob("*.json"):
+    q = await session.execute(
-        try:
+        select(Topic.name, sql_func.count(DocumentTopic.document_id))
-            meta = json.loads(p.read_text())
+        .join(DocumentTopic, DocumentTopic.topic_id == Topic.id, isouter=True)
-        except Exception:
+        .group_by(Topic.name)
-            continue
+    )
-        for t in meta.get("topics", []):
+    return {name: count for name, count in q}
-            counts[t] = counts.get(t, 0) + 1
-    return counts
 
 
 # ── Settings ──────────────────────────────────────────────────────────────────
+# Phase 2 will move per-user settings to users.ai_provider / users.ai_model
+# (D-03 deferred to user-scoped column population).
+# For now these remain as flat-file JSON — single-writer, no filelock needed.
 
 def load_settings() -> dict:
-    with _settings_lock:
+    """Read app settings from the flat-file SETTINGS_FILE.
+
+    Falls back to DEFAULT_SETTINGS if the file is missing.
+    # Phase 2 will move per-user settings to users.ai_provider / users.ai_model.
+    """
+    try:
         return json.loads(SETTINGS_FILE.read_text())
+    except (FileNotFoundError, json.JSONDecodeError):
+        return copy.deepcopy(DEFAULT_SETTINGS)
 
 
 def save_settings(settings: dict) -> None:
-    with _settings_lock:
+    """Write app settings to the flat-file SETTINGS_FILE.
+
+    No filelock — Phase 1 settings file is single-writer.
+    # Phase 2 will move per-user settings to users.ai_provider / users.ai_model.
+    """
     SETTINGS_FILE.write_text(json.dumps(settings, indent=2))
 
 
@@ -178,10 +441,33 @@ def mask_api_key(key: str) -> str:
 
 
 def settings_masked(settings: dict) -> dict:
-    import copy
     s = copy.deepcopy(settings)
     for prov in ("anthropic", "openai"):
         key = s.get("providers", {}).get(prov, {}).get("api_key", "")
         if key:
             s["providers"][prov]["api_key"] = mask_api_key(key)
     return s
+
+
+# ── Public surface ─────────────────────────────────────────────────────────────
+
+__all__ = [
+    "save_upload",
+    "save_metadata",
+    "get_metadata",
+    "list_metadata",
+    "delete_document",
+    "update_document_topics",
+    "remove_topic_from_all_documents",
+    "load_topics",
+    "save_topics",
+    "get_topic",
+    "create_topic",
+    "update_topic",
+    "delete_topic",
+    "topic_doc_counts",
+    "load_settings",
+    "save_settings",
+    "mask_api_key",
+    "settings_masked",
+]

backend/tests/conftest.py

@@ -41,14 +41,11 @@ def isolated_data_dir(monkeypatch, tmp_path):
     monkeypatch.setattr(config, "TOPICS_FILE", data_dir / "topics.json")
     monkeypatch.setattr(config, "SETTINGS_FILE", data_dir / "settings.json")
 
+    # Plan 04: services.storage is now async (PostgreSQL + MinIO).
+    # The flat-file _topics_lock / _settings_lock attributes no longer exist.
+    # Only SETTINGS_FILE is still used by the sync load_settings/save_settings.
     import services.storage as st
-    from filelock import FileLock
-    monkeypatch.setattr(st, "UPLOADS_DIR", data_dir / "uploads")
-    monkeypatch.setattr(st, "METADATA_DIR", data_dir / "metadata")
-    monkeypatch.setattr(st, "TOPICS_FILE", data_dir / "topics.json")
     monkeypatch.setattr(st, "SETTINGS_FILE", data_dir / "settings.json")
-    monkeypatch.setattr(st, "_topics_lock", FileLock(str(data_dir / "topics.json") + ".lock"))
-    monkeypatch.setattr(st, "_settings_lock", FileLock(str(data_dir / "settings.json") + ".lock"))
 
     yield data_dir
 

backend/tests/test_storage.py

@@ -20,7 +20,7 @@ import pytest
 # Test 1: object key matches STORE-02 regex
 # ---------------------------------------------------------------------------
 
-async def test_object_key_schema(db_session):
+async def test_object_key_schema():
     """STORE-02: put_object must return a key matching {user_id}/{doc_id}/{uuid4}{ext}."""
     try:
         from storage.minio_backend import MinIOBackend