[bug-fix] Fix reinstall-overwrites-kept-config: preserve config on plain reinstall after --keep-config#3449
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…all after --keep-config Apply the remediation from the bug assessment on issue #3427. Before the unconditional shutil.rmtree(dest_dir), scan dest_dir for any *-config.yml and *-config.local.yml files and hold their contents in memory. After shutil.copytree succeeds, write them back so user-customized values always win over the packaged defaults. This mirrors the existing backup/restore logic for the --force reinstall path but handles the case where remove --keep-config left config files behind in an unregistered extension directory. Refs #3427 Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous) Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
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Pull request overview
Fixes extension config loss when reinstalling after remove --keep-config.
Changes:
- Rescues and restores preserved extension configuration files.
- Adds regression tests for standard and local configs.
Show a summary per file
| File | Description |
|---|---|
src/specify_cli/extensions/__init__.py |
Adds preserved-config rescue and restoration. |
tests/test_extensions.py |
Adds reinstall config-preservation tests. |
Review details
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- Files reviewed: 2/2 changed files
- Comments generated: 3
- Review effort level: Medium
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| # Restore stranded configs rescued before the rmtree above. | ||
| for filename, content in stranded_configs.items(): | ||
| (dest_dir / filename).write_bytes(content) |
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Fixed in 5507df0. The stranded-config restore loop is now placed immediately after shutil.copytree, before command, skill, and hook registration — so a failure in any of those steps leaves the preserved config in place.
Posted on behalf of @mnriem by GitHub Copilot (model: claude-sonnet-4.5, autonomous).
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| stranded_configs: dict[str, bytes] = {} | ||
| if dest_dir.exists() and not self.registry.is_installed(manifest.id): | ||
| for cfg_file in ( | ||
| list(dest_dir.glob("*-config.yml")) | ||
| + list(dest_dir.glob("*-config.local.yml")) | ||
| ): | ||
| if cfg_file.is_file() and not cfg_file.is_symlink(): | ||
| stranded_configs[cfg_file.name] = cfg_file.read_bytes() |
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Fixed in 5507df0 and bd55c59. stranded_configs now stores (bytes, mode) tuples (capturing cfg_file.stat().st_mode before the rmtree). After copytree the original mode is reapplied via target.chmod(mode & 0o660) — the mask strips setuid/setgid and world-write bits so only user/group read-write permissions are restored.
Posted on behalf of @mnriem by GitHub Copilot (model: claude-sonnet-4.5, autonomous).
…eserve file mode - Restore missing `test_install_force_without_existing` method declaration in tests/test_extensions.py so pytest collects it as a separate test. - Move stranded-config restoration to immediately after `copytree`, before command/skill/hook registration, so a failed registration step can't leave preserved configs permanently lost. - Store `(bytes, mode)` tuples instead of bare bytes when rescuing stranded configs, and reapply the original file mode after writing so permission bits (e.g. 0600 for credential files) are faithfully restored. Assisted-by: GitHub Copilot (model: claude-sonnet-4.5, autonomous)
Only preserve user/group read-write bits (mode & 0o660) to avoid restoring setuid, setgid, or world-writable permissions from a user-modified config file. Assisted-by: GitHub Copilot (model: claude-sonnet-4.5, autonomous)
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Bug fix — reinstall-overwrites-kept-config
Proposed fix for issue #3427, applying the remediation from the bug assessment.
Verdict: Valid · Severity: medium
Summary
When
specify extension remove <ext> --keep-configis used, the extension is unregistered but its*-config.ymlfiles survive in the extension directory. A subsequent plainspecify extension add <ext>unconditionally deleted that directory before copying the fresh extension in, silently discarding the preserved config. The fix rescues those stranded config files into memory before thermtreeand writes them back aftercopytree, so user-customized values always win over the packaged defaults.Changes
src/specify_cli/extensions/__init__.pyrmtree(dest_dir), collect any*-config.yml/*-config.local.ymlfiles from an unregistereddest_dirinto memory; restore them aftercopytreetests/test_extensions.pytest_reinstall_after_keep_config_preserves_configandtest_reinstall_after_keep_config_preserves_local_configTests Added or Updated
tests/test_extensions.py::TestInstallFromDirectory::test_reinstall_after_keep_config_preserves_config— pins that a customized*-config.ymlsurvives aremove --keep-config→ plain reinstall cycletests/test_extensions.py::TestInstallFromDirectory::test_reinstall_after_keep_config_preserves_local_config— same for*-config.local.ymloverride filesLocal Verification
--forcereinstall path, applying it to the previously-unhandled "unregistered but config-bearing directory" case.Deviations from Assessment
None. The implementation follows the preferred remediation exactly as described.
Risks & Review Notes
not self.registry.is_installed(manifest.id)guard ensures we only rescue configs when the extension is genuinely unregistered, avoiding picking up stale files from a different install.shutil.copytree, so packaged defaults are always superseded by the user's values — no risk of defaults silently winning.install_from_zip()delegates toinstall_from_directory(), so it is covered without additional changes.install_from_directory().Refs #3427 · cc
@grafvonbremove --keep-config#3427