CU-8699upt9a Allow saving output onto disk when multiprocessing #52
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Make sure all the data is saved. That all the files are present. That the saved data is equal to the returned data.
…ches for saved data
mart-r
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Jul 18, 2025
* CU-8699upt9a: Add option to save multiprocessing output * CU-8699upt9a: Add a test for multiprocessing saved data. Make sure all the data is saved. That all the files are present. That the saved data is equal to the returned data. * CU-8699upt9a: Fix typo in output saving * CU-8699upt9a: Add more comprehensive multiprocessing tests with proper batching * CU-8699upt9a: Fix issue with limited number of jobs submitted per process. * CU-8699upt9a: Add a few more tests regarding multiprocessing with batches for saved data
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This PR allows one to save data to disk when multiprocessing.
The main goal was to leave the saved output as similar to v1's
cat.multiprocessing_batch_char_sizeas possible.It does so by adding a pair of new arguments to the
CAT.get_entities_multi_textsmethod:save_dir_path: Optional[str] = None- if specified, the path to be used for the databatches_per_save: int = 20- the number of batches to save at onceIn addition, it adds a new module
medcat.storage.mp_ents_savecat.pymoduleThere's also a minor test suite to make sure
annotated_ids.picklepart_<num>.pickle) are accounted forPS:
The PR also fixes a fundamental multiprocessing issue where not all the data was actually processed.
And adds more comprehensive tests to make sure that's not an issue going forward.