Refactor cleaning task and improve FSDB authentication#9
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- Updated `task.py` to handle FSDB authentication using `ROMI_DB_USER` and `ROMI_DB_PASSWORD` environment variables. - Added CLI arguments to allow passing `--db-user` and `--db-password` for FSDB login in `romi_run_task.py`. - Ensured that database credentials from CLI or environment variables are passed to the runtime environment in `run_task`. - Adjusted imports in `romi_run_task.py` for consistency and readability.
Description: - Replaced all occurrences of `from plantdb.commons.fsdb import FSDB` with `from plantdb.commons.fsdb.core import FSDB` in multiple files. - Adjusted dummy FSDB imports in test and task files to use `from plantdb.commons.test_database import dummy_db`. - Updated Jupyter notebooks to reflect the new import paths. - Ensured compatibility of downstream modules, scripts, and tasks with updated imports.
…`ValueError` - Import `FilesetExistsError` from `plantdb.commons.fsdb.exceptions` in `romitask/src/romitask/task.py`. - Update the `try/except` block when creating a fileset to catch `FilesetExistsError` and fallback to `fs_target.get()` for existing filesets.
…ated imports Signed-off-by: Arthur Luciani <arthur.luciani@ens-lyon.fr>
- Replaced `db.connect(unsafe=True)` with `db.connect()` across multiple files for safer database connections. - Updated import path for `compute_fileset_matches` to use `plantdb.server.core.utils` instead of `plantdb.server.rest_api`. - Fixed incorrect use of `sparse_pcd` for dense point cloud arrays in `plant3dvision/colmap.py`.
- Added `keep_pipeline_cfg` parameter to control removal of the `pipeline.toml` backup. - Introduced helper methods (`_merge_metadata_keep_list`, `_filesets_to_remove`, `_delete_filesets`, `_clean_images_metadata`, `_clean_orphan_json_files`, `_clean_orphan_directories`, `_remove_pipeline_backup`, `_confirm`) to modularize cleaning logic and simplify testing. - Replaced inline confirmation handling with `ask_confirmation` from `romitask.utils`. - Updated imports to include `Iterable` and the new `ask_confirmation` helper. - Fixed type annotation for `keep_metadata` (`luigi.listParameter`). - Streamlined metadata whitelist creation using the new helper. - Simplified fileset deletion and orphan metadata cleanup using the new static helpers. - Added optional pipeline backup removal controlled by `keep_pipeline_cfg`. - Improved logging messages and docstrings throughout the cleaning workflow.
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Refactor
Cleantask inromitask/task.py:keep_pipeline_cfgparameter to optionally retain thepipeline.tomlbackup._merge_metadata_keep_list,_filesets_to_remove,_delete_filesets,_clean_images_metadata,_clean_orphan_json_files,_clean_orphan_directories,_remove_pipeline_backup,_confirm) for clearer, test‑able logic.ask_confirmationfromromitask.utils.keep_metadata, logging, and docstrings.Refactor database usage:
db.connect(unsafe=True)calls to safedb.connect().Update import paths:
plantdb.server.core.utils.compute_fileset_matchesinstead of the REST API module.plantdb.commons.fsdb.FSDBwithplantdb.commons.fsdb.core.FSDBthroughout the project.Improve fileset creation error handling:
FilesetExistsError(imported fromplantdb.commons.fsdb.exceptions) instead of a genericValueError.Add environment‑based FSDB authentication and CLI support:
ROMI_DB_USERandROMI_DB_PASSWORDenvironment variables for login.--db-userand--db-passwordCLI arguments inromi_run_task.py.