fix(review): U3 atomic file writes for YAML + .env + skill config
All config file writes now use the write-temp + fsync + os.replace pattern (KTD-4) so a crash mid-write leaves the original file intact. - Add src/agentkit/server/utils/atomic_write.py with write_text_atomic - settings.py: _write_yaml_config and _write_env_var use atomic write - skill_service.py: import_skill uses atomic write - skill_service.py: update_skill_config uses atomic write + fcntl.flock around the read-modify-write cycle to serialize concurrent updates - Add 11 unit tests covering happy path, crash safety, concurrency, errors
This commit is contained in:
chiguyong
parent
698a8fafba
commit
4f261523c2
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@ -253,8 +253,11 @@ class SkillService:
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if not _is_within_directory(file_path, skills_dir):
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raise ValueError(f"Resolved skill path escapes skills_dir: {file_path}")
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with open(file_path, "w", encoding="utf-8") as f:
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f.write(yaml_content)
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# Atomic write (U3 — R6): write-temp + fsync + os.replace so a
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# crash mid-write doesn't leave a partial/corrupt YAML.
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from agentkit.server.utils.atomic_write import write_text_atomic
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write_text_atomic(file_path, yaml_content)
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if skill_registry is not None:
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try:
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@ -363,27 +366,46 @@ class SkillService:
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if not _is_within_directory(file_path, skills_dir):
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raise ValueError(f"Resolved skill path escapes skills_dir: {file_path}")
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# Read existing YAML, apply patch, validate, write back.
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with open(file_path, encoding="utf-8") as f:
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existing = yaml.safe_load(f) or {}
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# Read-modify-write with fcntl.flock to serialize concurrent
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# updates (U3 — R6). The lockfile is a sibling of the YAML so
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# it survives crashes and is visible to other processes.
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import fcntl
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if not isinstance(existing, dict):
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raise ValueError(f"Existing skill YAML at {file_path} is not a mapping")
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from agentkit.server.utils.atomic_write import write_text_atomic
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# Shallow merge: top-level keys in config_patch overwrite.
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# The 'name' field is preserved (cannot rename via patch).
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patched = {**existing, **config_patch, "name": existing.get("name", normalized)}
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lock_path = f"{file_path}.lock"
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with open(lock_path, "w") as lock_fh:
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fcntl.flock(lock_fh.fileno(), fcntl.LOCK_EX)
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try:
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# Read existing YAML, apply patch, validate, write back.
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with open(file_path, encoding="utf-8") as f:
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existing = yaml.safe_load(f) or {}
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# Validate the patched config by round-tripping through YAML.
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try:
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patched_yaml = yaml.safe_dump(patched, default_flow_style=False, allow_unicode=True)
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except yaml.YAMLError as exc:
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raise ValueError(f"Failed to serialize patched config: {exc}") from exc
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if not isinstance(existing, dict):
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raise ValueError(f"Existing skill YAML at {file_path} is not a mapping")
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_validate_yaml_content(patched_yaml)
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# Shallow merge: top-level keys in config_patch overwrite.
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# The 'name' field is preserved (cannot rename via patch).
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patched = {
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**existing,
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**config_patch,
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"name": existing.get("name", normalized),
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}
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with open(file_path, "w", encoding="utf-8") as f:
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f.write(patched_yaml)
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# Validate the patched config by round-tripping through YAML.
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try:
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patched_yaml = yaml.safe_dump(
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patched, default_flow_style=False, allow_unicode=True
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)
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except yaml.YAMLError as exc:
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raise ValueError(f"Failed to serialize patched config: {exc}") from exc
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_validate_yaml_content(patched_yaml)
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# Atomic write: write-temp + fsync + os.replace.
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write_text_atomic(file_path, patched_yaml)
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finally:
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fcntl.flock(lock_fh.fileno(), fcntl.LOCK_UN)
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# Reload the skill into the registry.
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try:
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@ -159,7 +159,14 @@ def _write_yaml_config(config_path: str, data: dict) -> None:
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Uses ruamel.yaml when available to preserve comments and formatting.
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Falls back to PyYAML otherwise.
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The write is atomic (write-temp + fsync + os.replace) so a crash
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mid-write leaves the original file intact (U3 — R6).
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"""
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import io
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from agentkit.server.utils.atomic_write import write_text_atomic
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original = _read_yaml_config(config_path)
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preserved = _reverse_resolve_env(data, original)
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try:
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@ -173,11 +180,13 @@ def _write_yaml_config(config_path: str, data: dict) -> None:
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original_data = yaml_writer.load(f)
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# Apply preserved values onto the ruamel-parsed structure
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_deep_update_ruamel(original_data, preserved)
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with open(config_path, "w", encoding="utf-8") as f:
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yaml_writer.dump(original_data, f)
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buf = io.StringIO()
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yaml_writer.dump(original_data, buf)
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write_text_atomic(config_path, buf.getvalue())
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except ImportError:
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with open(config_path, "w", encoding="utf-8") as f:
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yaml.dump(preserved, f, default_flow_style=False, allow_unicode=True, sort_keys=False)
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buf = io.StringIO()
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yaml.dump(preserved, buf, default_flow_style=False, allow_unicode=True, sort_keys=False)
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write_text_atomic(config_path, buf.getvalue())
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def _deep_update_ruamel(target: Any, source: Any) -> None:
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@ -207,9 +216,14 @@ def _write_env_var(config_path: str, key: str, value: str) -> None:
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If the key already exists in .env, its value is updated in place.
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If not, it's appended. Comments and formatting are preserved.
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The write is atomic (write-temp + fsync + os.replace) so a crash
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mid-write leaves the original .env intact (U3 — R6).
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"""
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from pathlib import Path
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from agentkit.server.utils.atomic_write import write_text_atomic
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env_path = Path(config_path).parent / ".env"
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lines: list[str] = []
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found = False
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@ -229,8 +243,7 @@ def _write_env_var(config_path: str, key: str, value: str) -> None:
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if not found:
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lines.append(f"{key}={value}\n")
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with open(env_path, "w", encoding="utf-8") as f:
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f.writelines(lines)
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write_text_atomic(env_path, "".join(lines))
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# Also set in current process so the next from_yaml resolves correctly
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os.environ[key] = value
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@ -0,0 +1 @@
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"""Server utility helpers."""
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@ -0,0 +1,88 @@
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"""Atomic file-write utilities (U3 — R6).
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Provides :func:`write_text_atomic` which writes text content to a file
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using the write-temp + fsync + os.replace pattern (KTD-4). This
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guarantees that:
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- A crash during the write leaves the original file intact (the temp
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file is abandoned).
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- Concurrent writers don't produce mixed content (``os.replace`` is
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atomic on POSIX).
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- The file's directory entry is durable after a crash (parent-dir
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fsync).
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The function is intentionally minimal — it operates on ``str`` content.
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Callers that need to serialize YAML/dict/etc. should do so before
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calling.
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"""
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from __future__ import annotations
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import os
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import tempfile
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from pathlib import Path
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def write_text_atomic(path: str | Path, content: str, *, encoding: str = "utf-8") -> None:
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"""Write ``content`` to ``path`` atomically.
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Flow:
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1. Write content to a temporary file in the same directory.
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2. ``fsync`` the temp file (data durability).
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3. ``os.replace(temp, path)`` — atomic rename on POSIX.
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4. ``fsync`` the parent directory (directory-entry durability).
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Args:
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path: Target file path. The parent directory must exist.
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content: Text content to write.
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encoding: Text encoding (default ``utf-8``).
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Raises:
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PermissionError: If the target directory or file is not writable.
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OSError: For other filesystem errors.
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"""
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target = Path(path)
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parent = target.parent
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parent.mkdir(parents=True, exist_ok=True)
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# Create the temp file in the same directory so os.replace stays
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# within a single filesystem (required for atomicity).
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fd, tmp_name = tempfile.mkstemp(
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dir=str(parent),
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prefix=f".{target.name}.tmp.",
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suffix=".partial",
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)
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tmp_path = Path(tmp_name)
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try:
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with os.fdopen(fd, "w", encoding=encoding) as f:
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f.write(content)
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f.flush()
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os.fsync(f.fileno())
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os.replace(tmp_path, target)
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# fsync the parent directory so the rename is durable.
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_fsync_dir(parent)
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except BaseException:
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# On any failure (including crash), clean up the temp file.
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# os.replace already succeeded → tmp_path no longer exists.
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try:
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tmp_path.unlink(missing_ok=True)
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except OSError:
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pass
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raise
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def _fsync_dir(path: Path) -> None:
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"""Best-effort fsync of a directory (POSIX only, no-op on Windows)."""
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if os.name != "posix":
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return
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try:
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dir_fd = os.open(str(path), os.O_RDONLY)
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try:
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os.fsync(dir_fd)
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finally:
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os.close(dir_fd)
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except OSError:
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# Some filesystems (e.g. network mounts) don't support fsync
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# on directories. Swallow rather than crash — the rename is
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# still atomic, just not guaranteed durable.
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pass
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@ -0,0 +1,202 @@
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"""Unit tests for atomic file-write utilities (U3 — R6).
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Covers:
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- Happy path: write_text_atomic writes correct content
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- Edge case: no temp file residue after success
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- Edge case: original file intact when write fails (mocked os.replace)
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- Edge case: concurrent writes don't produce mixed content
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- Error path: permission error on target directory
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- Integration: settings _write_yaml_config uses atomic write
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- Integration: settings _write_env_var uses atomic write
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"""
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from __future__ import annotations
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import os
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import threading
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from pathlib import Path
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from unittest.mock import patch
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import pytest
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from agentkit.server.utils.atomic_write import write_text_atomic
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# ---------------------------------------------------------------------------
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# Happy path
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# ---------------------------------------------------------------------------
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class TestWriteTextAtomic:
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def test_writes_content_correctly(self, tmp_path: Path):
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target = tmp_path / "output.yaml"
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write_text_atomic(target, "key: value\n")
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assert target.read_text(encoding="utf-8") == "key: value\n"
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def test_overwrites_existing_file(self, tmp_path: Path):
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target = tmp_path / "output.yaml"
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target.write_text("old: content\n", encoding="utf-8")
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write_text_atomic(target, "new: content\n")
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assert target.read_text(encoding="utf-8") == "new: content\n"
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def test_no_temp_file_residue(self, tmp_path: Path):
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target = tmp_path / "output.yaml"
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write_text_atomic(target, "key: value\n")
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# No temp/partial files should remain in the directory.
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residue = [
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f.name
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for f in tmp_path.iterdir()
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if f.name != "output.yaml" and not f.name.startswith(".")
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]
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assert residue == [], f"Unexpected temp files: {residue}"
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def test_accepts_str_path(self, tmp_path: Path):
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target = str(tmp_path / "output.txt")
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write_text_atomic(target, "hello\n")
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assert Path(target).read_text(encoding="utf-8") == "hello\n"
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def test_creates_parent_dirs(self, tmp_path: Path):
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target = tmp_path / "subdir" / "nested" / "output.yaml"
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write_text_atomic(target, "key: value\n")
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assert target.read_text(encoding="utf-8") == "key: value\n"
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# ---------------------------------------------------------------------------
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# Crash safety
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# ---------------------------------------------------------------------------
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class TestWriteTextAtomicCrashSafety:
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def test_original_intact_when_replace_fails(self, tmp_path: Path):
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"""If os.replace raises, the original file must be unchanged."""
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target = tmp_path / "output.yaml"
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target.write_text("original: true\n", encoding="utf-8")
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with patch("agentkit.server.utils.atomic_write.os.replace") as mock_replace:
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mock_replace.side_effect = OSError("simulated crash")
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with pytest.raises(OSError, match="simulated crash"):
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write_text_atomic(target, "new: true\n")
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# Original content must be intact.
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assert target.read_text(encoding="utf-8") == "original: true\n"
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# Temp file must be cleaned up.
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residue = [
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f.name
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for f in tmp_path.iterdir()
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if f.name != "output.yaml" and not f.name.startswith(".")
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]
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assert residue == [], f"Temp file not cleaned up: {residue}"
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def test_original_intact_when_fsync_fails(self, tmp_path: Path):
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"""If fsync raises (e.g. disk full), the original must be intact."""
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target = tmp_path / "output.yaml"
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target.write_text("original: true\n", encoding="utf-8")
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with patch("agentkit.server.utils.atomic_write.os.fsync") as mock_fsync:
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mock_fsync.side_effect = OSError("disk full")
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with pytest.raises(OSError, match="disk full"):
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write_text_atomic(target, "new: true\n")
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assert target.read_text(encoding="utf-8") == "original: true\n"
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# ---------------------------------------------------------------------------
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# Concurrency
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# ---------------------------------------------------------------------------
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class TestWriteTextAtomicConcurrency:
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def test_concurrent_writes_no_mixed_content(self, tmp_path: Path):
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"""Two threads writing different content — no mixed lines."""
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target = tmp_path / "output.yaml"
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target.write_text("init: 0\n", encoding="utf-8")
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barrier = threading.Barrier(2)
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results: list[bool] = []
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def writer(content: str) -> None:
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barrier.wait()
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write_text_atomic(target, content)
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results.append(True)
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t1 = threading.Thread(target=writer, args=("aaa: 1\nbbb: 2\nccc: 3\n",))
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t2 = threading.Thread(target=writer, args=("xxx: 1\nyyy: 2\nzzz: 3\n",))
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t1.start()
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t2.start()
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t1.join(timeout=5)
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t2.join(timeout=5)
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assert len(results) == 2
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# The final content must be one of the two writes, not a mix.
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final = target.read_text(encoding="utf-8")
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assert final in ("aaa: 1\nbbb: 2\nccc: 3\n", "xxx: 1\nyyy: 2\nzzz: 3\n")
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# ---------------------------------------------------------------------------
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# Error paths
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# ---------------------------------------------------------------------------
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class TestWriteTextAtomicErrors:
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def test_permission_error_on_unwritable_dir(self, tmp_path: Path):
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"""Writing to a read-only directory raises PermissionError."""
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ro_dir = tmp_path / "readonly"
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ro_dir.mkdir()
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os.chmod(ro_dir, 0o444)
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try:
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target = ro_dir / "output.yaml"
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with pytest.raises(PermissionError):
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write_text_atomic(target, "key: value\n")
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finally:
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os.chmod(ro_dir, 0o755)
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# ---------------------------------------------------------------------------
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# Integration: settings.py
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# ---------------------------------------------------------------------------
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class TestSettingsAtomicWrite:
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"""Verify that settings.py helpers use atomic writes."""
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def test_write_env_var_uses_atomic_write(self, tmp_path: Path):
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"""_write_env_var should write .env atomically (no partial writes)."""
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from agentkit.server.routes.settings import _write_env_var
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config_path = tmp_path / "agentkit.yaml"
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config_path.write_text("llm:\n default_model: gpt-4\n", encoding="utf-8")
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_write_env_var(str(config_path), "OPENAI_API_KEY", "sk-test-123")
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env_path = tmp_path / ".env"
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assert env_path.exists()
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content = env_path.read_text(encoding="utf-8")
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assert "OPENAI_API_KEY=sk-test-123" in content
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# No temp files should remain.
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residue = [
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f.name
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for f in tmp_path.iterdir()
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if not f.name.startswith(".") and f.name != "agentkit.yaml"
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]
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assert residue == [], f"Unexpected files: {residue}"
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def test_write_env_var_preserves_existing_content(self, tmp_path: Path):
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"""Updating an existing key preserves other lines."""
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from agentkit.server.routes.settings import _write_env_var
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config_path = tmp_path / "agentkit.yaml"
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config_path.write_text("llm:\n default_model: gpt-4\n", encoding="utf-8")
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env_path = tmp_path / ".env"
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env_path.write_text(
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"# Header comment\nOPENAI_API_KEY=old-value\nANTHROPIC_API_KEY=sk-ant\n",
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encoding="utf-8",
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)
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_write_env_var(str(config_path), "OPENAI_API_KEY", "new-value")
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content = env_path.read_text(encoding="utf-8")
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assert "# Header comment" in content
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assert "OPENAI_API_KEY=new-value" in content
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assert "ANTHROPIC_API_KEY=sk-ant" in content
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assert "old-value" not in content
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