Improve PATIENT/PERSOON processing and more #144
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Beware! `poetry.lock` is not up-to-date in this commit (and most recent commits wouldn't work with the current last released version of `docdeid`, anyway).
Leaving the test case commented out for now. This won't be a frequent problem but it's something I noticed when first trying out this tool.
Otherwise, random names are labeled as "patient", which will be wrong in most cases.
...and use it to determine where patient name is to be merged with a neighbouring person mention and when not.
...as required by pylint.
This makes Pylint happier and the code simpler.
This is needed so as to reduce the number of arguments for the `_match_sequence` method and creates a cleaner inheritance hierarchy between annotators, too.
This bug sent Deduce into an endless loop. I wonder whether that's still possible with carefully crafted inputs, and something to be fixed.
This is a change I had locally and surfaced during merge conflict resolution, which may be necessary for some tests to work (and by extension to the system at runtime, too).
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This is the result of my first encounter with this codebase (Docdeid and Deduce), the second part (Deduce). My goal was to understand the inner workings of it and then make sure that capitalized street names are pseudonymized (all-caps or titlecased, and covering also the special case of the "IJ" digraph in Dutch). When at it, I noticed unexpected behaviour for patient names v. other person names and improved that as well.
This depends on changes in Docdeid, filed as vmenger/docdeid#20.
To use that Docdeid version, I checked out the two repos side by side and added the following configuration in Deduce's
pyproject.toml:FWIW, I also see a diff in my local (non-committed) version of
base_config.jsonaffecting "initiaal_patient" mentions but it's been 4 months since I intensively worked on this codebase so I don't remember anymore whether it's useful or even necessary anymore. But if some tests fail without it for you, let me know, this may well be the reason.