Harden runtime and add backup foundation

tests/test_backup.py

@@ -0,0 +1,71 @@
+"""Tests for runtime backup creation."""
+
+import json
+import sqlite3
+from datetime import UTC, datetime
+
+import atocore.config as config
+from atocore.models.database import init_db
+from atocore.ops.backup import create_runtime_backup
+
+
+def test_create_runtime_backup_copies_db_and_registry(tmp_path, monkeypatch):
+    monkeypatch.setenv("ATOCORE_DATA_DIR", str(tmp_path / "data"))
+    monkeypatch.setenv("ATOCORE_BACKUP_DIR", str(tmp_path / "backups"))
+    monkeypatch.setenv(
+        "ATOCORE_PROJECT_REGISTRY_PATH", str(tmp_path / "config" / "project-registry.json")
+    )
+
+    registry_path = tmp_path / "config" / "project-registry.json"
+    registry_path.parent.mkdir(parents=True)
+    registry_path.write_text('{"projects":[{"id":"p01-example","aliases":[],"ingest_roots":[{"source":"vault","subpath":"incoming/projects/p01-example"}]}]}\n', encoding="utf-8")
+
+    original_settings = config.settings
+    try:
+        config.settings = config.Settings()
+        init_db()
+        with sqlite3.connect(str(config.settings.db_path)) as conn:
+            conn.execute("INSERT INTO projects (id, name) VALUES (?, ?)", ("p01", "P01 Example"))
+            conn.commit()
+
+        result = create_runtime_backup(datetime(2026, 4, 6, 18, 0, 0, tzinfo=UTC))
+    finally:
+        config.settings = original_settings
+
+    db_snapshot = tmp_path / "backups" / "snapshots" / "20260406T180000Z" / "db" / "atocore.db"
+    registry_snapshot = (
+        tmp_path / "backups" / "snapshots" / "20260406T180000Z" / "config" / "project-registry.json"
+    )
+    metadata_path = (
+        tmp_path / "backups" / "snapshots" / "20260406T180000Z" / "backup-metadata.json"
+    )
+
+    assert result["db_snapshot_path"] == str(db_snapshot)
+    assert db_snapshot.exists()
+    assert registry_snapshot.exists()
+    assert metadata_path.exists()
+
+    with sqlite3.connect(str(db_snapshot)) as conn:
+        row = conn.execute("SELECT name FROM projects WHERE id = ?", ("p01",)).fetchone()
+    assert row[0] == "P01 Example"
+
+    metadata = json.loads(metadata_path.read_text(encoding="utf-8"))
+    assert metadata["registry_snapshot_path"] == str(registry_snapshot)
+
+
+def test_create_runtime_backup_handles_missing_registry(tmp_path, monkeypatch):
+    monkeypatch.setenv("ATOCORE_DATA_DIR", str(tmp_path / "data"))
+    monkeypatch.setenv("ATOCORE_BACKUP_DIR", str(tmp_path / "backups"))
+    monkeypatch.setenv(
+        "ATOCORE_PROJECT_REGISTRY_PATH", str(tmp_path / "config" / "project-registry.json")
+    )
+
+    original_settings = config.settings
+    try:
+        config.settings = config.Settings()
+        init_db()
+        result = create_runtime_backup(datetime(2026, 4, 6, 19, 0, 0, tzinfo=UTC))
+    finally:
+        config.settings = original_settings
+
+    assert result["registry_snapshot_path"] == ""

tests/test_database.py

@@ -0,0 +1,49 @@
+"""Tests for SQLite connection pragmas and runtime behavior."""
+
+import sqlite3
+
+import atocore.config as config
+from atocore.models.database import get_connection, init_db
+
+
+def test_get_connection_applies_busy_timeout_and_wal(tmp_path, monkeypatch):
+    monkeypatch.setenv("ATOCORE_DATA_DIR", str(tmp_path / "data"))
+    monkeypatch.setenv("ATOCORE_DB_BUSY_TIMEOUT_MS", "7000")
+
+    original_settings = config.settings
+    try:
+        config.settings = config.Settings()
+        init_db()
+        with get_connection() as conn:
+            busy_timeout = conn.execute("PRAGMA busy_timeout").fetchone()[0]
+            journal_mode = conn.execute("PRAGMA journal_mode").fetchone()[0]
+            foreign_keys = conn.execute("PRAGMA foreign_keys").fetchone()[0]
+    finally:
+        config.settings = original_settings
+
+    assert busy_timeout == 7000
+    assert str(journal_mode).lower() == "wal"
+    assert foreign_keys == 1
+
+
+def test_get_connection_uses_configured_timeout_value(tmp_path, monkeypatch):
+    monkeypatch.setenv("ATOCORE_DATA_DIR", str(tmp_path / "data"))
+    monkeypatch.setenv("ATOCORE_DB_BUSY_TIMEOUT_MS", "2500")
+
+    original_settings = config.settings
+    original_connect = sqlite3.connect
+    calls = []
+
+    def fake_connect(*args, **kwargs):
+        calls.append(kwargs.get("timeout"))
+        return original_connect(*args, **kwargs)
+
+    try:
+        config.settings = config.Settings()
+        monkeypatch.setattr("atocore.models.database.sqlite3.connect", fake_connect)
+        init_db()
+    finally:
+        config.settings = original_settings
+
+    assert calls
+    assert calls[0] == 2.5